Won't boot up in Windows 7 partition anymore

I bought my mac mini about two months ago and had no problems of any kind, including installing Windows 7 on it through boot camp.
Today I was working on the Windows 7 side of the partition on some flash sites in a program I use called SwishMax 3. Now this program has its own files called .swi files. I have a number of these files on my computer.
I had been working in and out of this program all day until at one point I went to open an .swi file and couldn't find any. I looked in every folder they could be in and they were all suddenly gone where they had just been all there minutes ago.
I decided to reboot the mac mini to see if the files would be restored but it never got to the Windows desktop...It's just stuck at "Starting Windows"...I have since done a force shut down..
I rebooted the computer and got into the Snow leopard partition with no problem, though.
But while in the snow leopard side, I noticed that the windows all appeared stretched which to me is an indicator that something needs to be updated.
After failing to complete two updates, I just clicked the prompt that came up that said "finish" and the mac shut itself down.
I am going to call Apple support tomorrow but I was wondering if anyone had any insight or similar experience?
I'm trying to determine if the Swishmax software had something to do with this or if it's just an update issue?
I haven't installed any updates on the apple partition since I first bought the computer because I mostly use the windows side on account that the swishmax software only works with Windows.
Thanks.
Message was edited by: chillspike

The problem just....went away....lol.

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