The problem with Gnotella not connecting is related to the default host used by 1.0.0 not operating any longer, there are many others that operate. There is also a new beta version available at http://www.gnotella.com/beta that solves this problem.

In terms it messing up your computer that seems extremely unlikely as it does not touch any system files that the programs you mention use. I was wondering, if it might be more likely that the Campus T1 you mention has possibly picked up a little activity in the past few days as I imagine an influx of students around this time have bombarded it with a large amount of data. You can also view the exact files Gnotella installed in the uninsXXX.dat file in the Gnotella directory.

The Litestep tray icon problem is hopefully addressed in the beta I mentioned previously as well.

Shaun