Try deleting your LW preferences folder whilst LW is closed; found here /Users/your_username/Library/Preferences/LimeWire
It will mean next time you start LW up, you will be asked to re-set your options such as as downld location, speed selection, etc.
You might also consider this
Tip: Purge the Downloads Queue! if you have many incompletes. It will be difficult to restart the older incompletes with the newer version. eg: delete those that are 0% & 0 - 50 KB
BTW which browser did it happen to you when it opened up the Napster site? Explorer right?