Well, it is not that Macs can't get viruses or SpyWare, it is just that the chance is the same as a plain crash, not all that common, but it can happen. I have heard that there are several problems while running Windows through boot camp, one of those could be your problem, personally, I would never put Windows on my computer, I just don't need to. Plus while running Windows, means that you will have to get virus software event though it is running on a Mac. Same hardware, different software, big difference. So I would not be surprised at all if there is a loop hole going on with your computer and Windows. Hackers have now found a way to ruin the computer of a Mac while it is running on Windows, and you know that they are going to take advantage of that. If I were you, take of Windows, and try to see if your speed it changed, if it is, try to keep Windows off, if it doesn't, well consider putting it back on.
Good Luck, Hope your computer gets well soon!