This usually means that the invisible Finder Desktop files that match documents to applications is missing a connection.

There are a few things you can do.
First--make sure your stuffit is up to date. You can always drag the .sits onto stuffit expander to open them. With luck, this will set the expander prefs automatically, otherwise go into the stuffit expander prefs to set stuffit to open the .sits.

Rebuilding the desktop (holding down command and option just before the hard drive loads onto the desktop in the startup sequence) is another way to match applications and their files (thought this was unnecessary in OS 9).

Then, get the latest LimeWire. The developers have made lots of good changes since 2.9.8

Cheers--nice clear first post!