[bjgregory]

You won't find virus software for Ubuntu. Unix/Linux was designed with security in mind from the start, user permissions and so on. You have to switch user to the superuser to do any real damage to a Linux installation, even deliberately. Of course, it's possible to install programs that use exploits to get around this but the nature of open source software means that security holes are quickly fixed (sometimes within hours). My dad had this same problem, we spent ages looking for software to fix Windows from Ubuntu on his machine, couldn't find a thing. I guess it's not a priority of Linux users to write programs to fix Windows installations. :p
What you COULD do is boot into Ubuntu, download a trojan remover, move it onto your Windows partition and then boot back into Windows and run it. Try that and tell me if it works, and if you need any help with those steps give me a shout.