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Help locating possible trojan or other virus
So my saga with possible viruses continues...while playing a game with a friend just a few minutes ago, my computer took on a mind of its own and began opening strange command prompts as if they were cd'ing to the locations of other games, as well as moving the mouse around, opening windows, etc. My immediate reaction was close everything not necessary (i.e. the skype call, the game, itunes, etc), open task manager, search it, and unplug the internet connection, to see if I couldn't catch something in the act. However, I found nothing.
Possible viruses always confuse me, because I am usually careful about what I download, where I visit and what I give access to, and the only programs I have installed recently have come from sites or developers I trust. Once again I ran scans, malware bytes and MSE, I found nothing. I found nothing extraordinary running, no odd tasks in the task scheduler, no strange programs installed, everything seems perfectly fine. And yet my computer behaved as though there was a second entity controlling it, be it a remove access or automated program, or some weird-ass glitch bug thing that made windows do random things (yeah right...). Everything which occurred could perhaps have happened if my mouse/keyboard drivers had a fit, its not like the mouse movements seemed to have a purpose, and everything which opened I have on my taskbar or in other easy to reach places which were displayed at the time.
Does anyone know what this may have been, where it may be lurking, or what I could do?
Thanks,
Tom