I have exactly the same setup as yours (java 1.4.2_03/Fedora/VFAT Shared folder/over 550 files), however I don't see the problem. What exactly do you mean by scanning?

At startup LimeWire does check the folders for new or changed files (which is very local I think), however this only takes a second on my system and happens when the system is already under stress from starting the program anyway.

If it's this you're really going to have to live with it I think, however if you're meaning that LimeWire has to calculate the checksums everytime, there's something wrong.