Just a few hours ago my gnome fortress had a sheer drop in FPS, from steady 150 down to 30 or so. I tried using fix/item-occupancy, and it listed a hell long list of items of "invalid pos", and told me that the problem was so severe that it could not fix it. As I know some of DF's memory layout, I then made a small application to peek into the memory, and found that in the block where my auto woodcutter was in (namely block at 32, 96, 53), there was thousands of items that should be at z-level 54. I thought that could be these item are being transferred by the drilling rig upstairs so I let one gnome pulled the lever and stopped the woodcutter and the drilling rig. but after some time, those items were still in z-level 53. I suspect this let the game code break and thus kill the FPS.
As the test went further, I found that when the save was first loaded there are no item misplacements but as every tick went a new item had become misplaced. After removing all reagents and output from the woodcutter there are no further increase of misplaced items. So I suspect that it could be the drilling rig sucks the output to the level above but failed to remove references in the level below.
The woodcutter is running in the save, load the save and run the game for a while, then you should notice the FPS drop.
The save was created in Masterwork 5.05, but after updating to 5.10, the problem remains.