I need to know which repair you are talking about. When you run them you will see a lot of bat files run. This is normal. And the reset permissions one will show a lot of information as it works, again all normal
I run my windows repair on a TON of machines and have computer shops that use it daily. Never heard of the problem you had.
Sounds more like a side effect of something, but I don't want you to chance it again, if your working let it be
This is why in the program I have users make some sort of backup. Every system is different and no telling exactly how things will go with what people have installed. 99% of the time everything works great. But as with any program every now and then you hit a system that has something different about it and something gets tripped up. Best thing to do is always have a backup before doing anything big with the system.
Shane