Should I just leave my computer on tonight so as to not give the files a chance to 'transform' into another file?
If possible, yes.
Am I compromising our network here at work in any way?
Possibly; spyware and adware infections do not spread over networks, but viruses/trojans/worms obviously do. However, if your machine is infected by network-spread infected, chances are very good that you're not the only one (or the first one) who's been hit.