May have a Boot Sector Virus?

So I did a Factory Restore on my Computer cause it was goin slow, DVD Back Ups going slow, DVD Shrink Going Slow. When I open a program it sometimes opens slow. So After it restored it and installed windows, It said on the Screen Boot Sector Virus.

This may the reason Been having Computer Problems. I downloaded this the Avira Boot Sector Repair Tool and burned the ISO to CD and did a reboot to that. But all it did was stay on a black screen, so I didnt know if it was working or what it was doing,

The Computer is pretty New. Got it in Late January 09.  Its a Gateway Model RS780. Im also running Windows Vista.

So Im hoping someone here with more knowledge about Virus can Help me out. Any help is great. thanks.

[Moderator]

Boot sector viruses are very rare. WHAT gave you a message saying you have one?