Usually LimeWire analyzes each file only once and then saves the data to a file called "fileurns.cache" so at the next startup LimeWire can just read the data it saved without having to rehash each shared file. Somehow LimeWire doesn't seem to do so correctly. Does LimeWire save your preferences correctly?

If not, there might be a problem with your preferences folder which is usually:
[home]/.limewire

LimeWire will need writing access to that folder.