Have you noticed that the market is not exactly flooded with Java apps for the Macintosh? There are reasons.

Assigning Limewire almost twenty times the minimum RAM is a needless waste of your computer's resources.

It doesn't matter if apps are open when you change the appearance manager. Why Charcoal? Why not the old standard default Chicago??

The default location for MRJ is *not* Applications, but System Extensions and Program support within that. If, however, the sys CD you used for the clean install did not have the latest MRJ, then it was overwritten with the previous version. Unless you have moved it, it will have installed in the proper place.

Rebuilding the desktop is always good maintenance. Zapping the PRAM basically gives you something to do, but actually resolves few problems.

I would check the MRJ version, then reinstall the latest Limewire. If that doesn't work, perhaps you can find an earlier version or wait for he next one to be released.