Try doing the following: Start Limewire, start a couple of random downloads and close it again. If the downloads.dat in your shared directory has a size of 375 bytes (or a similar value, since it might differ from version to version) it is empty, which means LimeWire was unable to write it. (Check file permissions in that case).

If it was written, but still it is not read after restart, I don't know what happened. I don't know that kind of behaviour from the official LimeWire-version. The latest CVS-code seems to incorporate that bug, but that hasn't been released yet.

Are you using AquaLime or CleanLimeWire?