It's generally due to Java.
10.3.9 issues (click on link) And also try deleting your LW preferences found here: /Users/your_username/Library/Preferences/LimeWire
I also run 2 mac osx's & os 9 on my comp. I've never had the same issues though. I presume you have the 2nd OSX on a different HDD or partition right?! I think that's advisable.