Hmm. You're right--incompletes >0k should resume on startup. There was a problem for a while, especially after a crash, but should be fixed now.
Does Acq still set the incomplete folder inside the shared folder? Perhaps your old Acq prefs/folders and new LimeWire prefs/folders are a problem. If you can afford a clean install, might be worthwhile to do a finder search for the Acq and LW folders (including any "incomplete" folders) and start fresh.
btw--check out Jens-Uwe's cvs build of LW
http://baghira.han.de/~jum/LimeWire.html
cheers