I had a bad time with some Viruses and spyware / malware last week too. One of then was Trojan.win32... also Some things that seemed to help me eventually get rid of it were:
1.) Build a Bart PE spyware CD with free virus tools, like McAfee Stinger and others. See irongeek.com/i.php?page=security/pebuildertutorial. Scan your drive and get rid of as much as you can. I had some trouble getting all the plugins right, so had the best luck just putting the standalone scanners on a memory stick, and making sure the BartPE had the HWPnP so it would detect the USB drive. Get the command version of scanners, McAfee stinger, hijack this, and whatever else you can get that can be run without being installed and put it on the USB drive.
2.) Install Microsoft® Windows® Malicious Software Removal Tool (KB890830)
3.) Install Spybot search and destroy. It has a real-time protection that alerts you when anything trys to change the registry. This is important because the malware I had kept re-installing itself every minute, or every time I clicked on the warning box you are talking about. I would delete all the files found by spyware scanners, and within a minute or two, they’d be back. When it alerts you of a registry change be very careful what you choose, whether to allow or block it. In the box that pops up, in the middle fo the bottom, there is a button that brings up info on the change. If it says it is spyware or malware, then block the change and click the box to remember it.
4.) Install Windows Defender (requires Validation)
5.) If none of these works, if you have a second hard drive, install a second copy of windows to that other drive. Boot to it and install virus and spyware scanners and try to clean your hard drive as best you can. Then do 1 - 4 above, if they didn’t work the first time.
This is really no fun at all. But I was sure happy when I got through it.
I really didn’t make much progress until I ran the Windows tools 2.) and 3.).
Once you get it clean..
grisoft.com has a free virus scanner for home use.
F-prot has one also.
Check on Download.com for others.