Ok, I know exactly what's going on. xD
However, I don't think that you're getting any less logs then normal, possibly you cut down a few small trees when you noticed the difference and that might have freaked you out a bit.
As some know, we've been having severe lag spikes on the server, especially with 10 plus people online. Now, in an attempt to fix this, we had contacted our hosters with the problem, and they came in, and did a lot of stuff to fix up the server. One of the things they did was install spigot, which is a more efficient, less laggy, and more optimized version of craft bukkit. One of the options that spigot installed with itself was the ability for blocks to condense, much like natural minecraft already condenses blocks, but spigot takes it to a much greater level allowing the condensing of blocks from much farther away then normally noticed or possible. The original condensation was probably half a block, or 0.5 distance. Now the condensation of blocks is 1.0 distance. Which allows the piles of blocks to be condensed into single items. Note, that this effect is primarily graphical, and it also helps out the server, as well as the player due to the fact that rendering costs are cut down dramatically. There should not be any effect on actual dropped items.
If people continue to notice a calculated effect on the actual dropped items, as in fewer items dropping, I will investigate it further. However there should be no effect on how many items it drops, just an effect on how many items are visually seen.