My Computer Scare

I just had a big time scare of losing all my documents on my computer.
I had been getting this stupid notice on my computer telling me my Windows version may be counterfeit etc...
Well I had accidentally hit yes to a windows box I should had clicked no to and have had this issue for a few months while my brother was in the moving stage to the new house they bought.
He finally found the Windows disc and I reloaded it this am only to have even more troubles!
Luckily he was in town and came by to patch things up and resolve the dilemma.
The issues still resides in the CPU, but after resetting everything we were able to disable the notices.
All I can tell any of you is make certain you read any window before clicking yes!
What hassles from HELL!