Ive been using TuneUp Utilities for almost 2 years now and have no problems like that.
You can use "Rescue Center" to undo any changes you made with TuneUp.
If youre using "TuneUp MemOptimizer", STOP.
If youre using "1 Click Maintenance", DON'T.
Open "TuneUp System Optimizer" and use "View Tips...