Are you using the registry cleaning feature of Tune Up Utilities? Many of us on the forums actually do not recommend automated optimization tools for Windows 7. Windows 7 does a much better job of handling its own optimization than its predecessors did. We especially do not recommend registry cleaning as an "optimization" step because automated registry cleaning causes more harm to the registry than it actually repairs.
In the future, if you need help optimizing Windows 7, please post a thread in
Performance & Maintenance - Windows 7 Forums or follow the tutorial enclosed in that forum to
Optimize Windows 7.
See if you can do a
System Restore to before the problems began. Then uninstall Tune Up Utilities, or stop using its registry cleaning feature. More than likely, your registry has been compromised by the software and any more repairs will just make matters worse. Let us know if System Restore resolves the issue.