I have no problems with using my scrollwheel with any of the panes in FlashFXP. Here are my system specs:
-Logitech Cordless Freedom 3-button mouse w/ scrollwheel, using PS/2 port
-Logitech Mouseware Driver v9.41.1
-FlashFXP v2.0 Build 906
-Office Compatible scrolling is disabled
If you need any more specs, just ask
