Your best chance at solving this mystery is to focus on your hacked machine, how it was accessed, any malware that is on it. Mostly it sounds like you didn't secure your machine properly, in which case your chance of fixing this disaster will sadly be very small.
I believe it must have been a virus of some sorts. Yes you are right. I don't think I can do anything at this point. Format and reinstall windows is the best I can do, and from there on not ever use windows for any security sensitive sites/systems.
Don't format your windows compute it's evidence that someone can use to find the perps! Use vmware conversion program to convert it to a VM so you have all the logs and events. But if you can keep the HD as they may have only deleted a evidence file and not obliterated it thus you could undelete the file.