Fossil trees trunks, which extend upward through multiple layers of limestone, have been found in many areas of the world including Kingston, Ontario [there are no such trees in Kingston, Ontario -AM] and Joggins, Nova Scotia [emphasis added].
This suggests that these very thick deposits were deposited very rapidly. Similar polystata trees have been found extending upright through successive seams of coal. Some of these trees have supposedly stood upright while successive cycles of oceans and peat swamp have pasted through an area. You be the judge as to the most logical interpretation... slow accumulation over thousands of years or... rapid burial during a massive world wide flood.
One of the best, and longest-known "fossil forest" occurrences is a locality known as Joggins, in Nova Scotia. It is Carboniferous in age, and was first described in detail in the late 1800s. Here is a quote from Dawson 1868 (pp. 179-180) on the nature of the trees at this locality, in a beautiful cliff section over 1km thick:
"In the [stratigraphic] section in the preceding chapter, the reader will observe the words "Underclay, Stigmaria [a type of fossil tree trunk]" frequently recurring; and over nearly every underclay is a seam of coal. An underclay is technically the bed of clay which underlies a coal-seam; but it has now become a general term for a fossil soil [Dawson's emphasis], or a bed which once formed a terrestrial surface, and supported trees and other plants; because we generally find these coal underclays, like the subsoils of many modern peat-bogs, to contain roots and trunks of trees which aided in the accumulation of the vegetable matter of the coal. The underclays in question are accordingly penetrated by innumerable long rootlets, now in a coaly state, but retaining enough of their form to enable us to recognize them as belonging to a peculiar root, the Stigmaria, of very frequent occurrence in the coal measures, and at one time supposed to have been a swamp plant of anomalous form, but now known to have belonged to an equally singular tree, the Sigillaria, found in the same deposits (Fig. 30). The Stigmaria has derived its name from the regularly arranged pits or spots left by its rootlets, which proceeded from it on all sides. The Sigillaria has been named from the rows of leaf-scars which extend up its trunk, which in some species is curiously ribbed or fluted. One of the most remarkable peculiarities of the stigmaria-rooted trees was the very regular arrangement of their roots, which are four at their departure from the trunk, and divide at equal distances successively into eight, sixteen, and thirty-two branches, each giving off, on all sides, an immense number of rootlets, stretching into the beds around, in a manner which shows that these must have been soft sand and mud at the time these roots and rootlets spread through them.
It is evident that when we find a bed of clay now hardened into stone, and containing the roots and rootlets of these plants in their natural position, we can infer, 1st, that such beds must once have been in a very soft condition; 2ndly, that the roots found in them were not drifted, but grew in their present positions; in short, that these ancient roots are in similar circumstances with those of the recent trees that underlie the Amherst marshes [these are local tidal marshes, some with recently-buried forest layers in the peat and sediment]. In corroboration of this, we shall find, in farther examination of this [stratigraphic] section, that while some of these fossil soils support coals, other support erect trunks of trees connected with their roots and still in their natural position."
There is very little, with the exception of terminology, that would be different in a "modern" interpretation of these features, and Dawson has much more detail on the other sedimentological features found at Joggins that support his interpretation. Dawson records well over a dozen horizons with large upright trees, and smaller ones are even more common. The section at Joggins can still be visited today, and is particularly well-known for the small reptile fossils found there (they often occur inside the upright tree stumps, apparently they fell in the hollow stump). There are usually a few upright trees exposed on the shore, although the rapid erosion of the 10m+ high cliffs means the exposed examples change every year.
Given that an "in place" occurrence was convincingly determined by observations made in the 19th century for this and many other "fossil forest" localities, it is surprising that these conclusions have not been recognized by modern "young Earth global flood" [YEGF] creationists as clear evidence of non-global-flood deposition for much of the geologic record. They often hinge their current arguments on the occurrence of upright trees in Yellowstone National Park, point to their volcanic setting, and then point to floating upright trees floating in Spirit Lake near Mt. St. Helens , and say, "See? They could be transported during the flood.". This argument is completely fallacious, because most "fossil forests" do not occur in volcanic deposits, and do have the fragile roots of the stumps tightly penetrating into the surrounding sediment, often into a paleosol (fossil soil) [besides Joggins, see also 3]. One occurrence is even associated with dinosaur footprints on the same surface, on top of a coal seam [4, 5, 6]. The "transported floating upright stumps" model  is a complete red-herring that does not apply to the vast majority of "fossil forest" occurrences.
As for Malone's "problem" with the "thousands of years" for the tree to remain upright for "slow accumulation" to occur, it is a non-problem - he is simply interpolating the average depositional rates for an entire formation down to the scale of metres. This is not the correct way to do it, because individual beds can be deposited rapidly (say, sands and mud during a levee breach), and then little deposition can occur for a long time (e.g., a soil horizon), as is observed in modern river floodplain environments where trees commonly occur. In short, he is assuming conventional geologists would interpret the occurrence the simple way he has interpolated - they do not.
One of the most compelling features of Dawson's comments, from a YEGF creationist's perspective, may be the closing remarks of his book, in the conclusion section on p.671. Statements expressing similar sentiments can be found in most geological books of the period (e.g., Murchison's "Siluria", where the Silurian and other Paleozoic systems are first defined):
"Patient observation and thought may enable us in time better to comprehend these mysteries; and I think we may be much aided in this by cultivating an acquaintance with the Maker and Ruler of the machine as well as with His work."
Dawson has no theological problems with the conclusions he drew, which are basically similar to the ones drawn by geologists now. Many other geologists of the period were devoutly religious, and clearly expressed the fact in their publications.
Apparently, many 19th century geologists share a common philosophical framework with modern creationists, but, strangely enough, modern creationists come to completely different conclusions from both the 19th century geologists and current geologists. The common appeal by modern creationists to an "atheistic" or "humanistic" philosophical framework that "taints" the interpretations of science is quite ridiculous in light of the strong beliefs of many historical scientists, particularly in geology. Why should creationists still have a problem with their conclusions, more than 100 years later?
Malone, along with many "young Earth global flood creationists, have no idea that even data from the 19th century, presented by a creationist geologist is enough to demolish the "polystrate fossil trees" part of their presentation. "Polystrate fossil trees" are probably one of the weakest pieces of evidence YEGF creationists can offer for their interpretation. I wish they would stop using it.
 Coffin, H.G., 1983. Erect floating stumps in Spirit Lake, Washington. Geology, v.11, p.298-299.
 Cristie, R.L., and McMillan, N.J. (eds.), 1991. Tertiary fossil forests of the Geodetic Hills, Axel Heiberg Island, Arctic Archipelago, Geological Survey of Canada, Bulletin 403, 227pp.
 Parker, L.R. and Balsley, J.K., 1989. Coal mines as localities for studying dinosaur trace fossils. IN: Gilette, D.D. and Lockley, M.G. (eds.), Dinosaur Tracks and Traces. Cambridge University Press:Cambridge, p.354-359.
 Parker, L.R. and Rowley, R.L., Jr., 1989. Dinosaur footprints from a coal mine in east-central Utah. IN: Gilette, D.D. and Lockley, M.G. (eds.), Dinosaur Tracks and Traces. Cambridge University Press:Cambridge, p.361-366.
 Carpenter, K., 1992. Behaviour of hadrosaurs as interpreted from footprints in the "Mesaverde" Group (Campanian) of Colorado, Utah, and Wyoming. Contributions to Geology, University of Wyoming, v.29, no.2, p.81-96. [ This one has a map of the dinosaur footprints and stumps - fig. 1 ]