Hey abro89,
Unfortunately system repair tools can sometimes do this. These tools by definition modify sensitive parts of your system, e.g. the Registry and other system files, and the simple reason things can go wrong is that Windows is extremely complex. Consider that some versions of Windows file will change every Tuesday when there is a new update from MS - system repair tools have to be aware of every single version of every single system file, and every single registry combination.
This is already hundreds of thousands of files and registry configs the tools need to keep in mind - then add in thousands more to this due to the number of different languages that Windows supports (different language packs come with a whole bunch of new files) and you can quickly see how it's hard for any single tool to be perfect 100% of the time. Even MS screws this up now and then!
Typically we recommend avoiding these types of repair tools due to the historically high incident rate that users encounter with them. Some of them are a bit safer than others, but they all suffer from the complexity problem. It's great you ran a backup before using the tool.
Are you still encountering issues that need resolving?
