I was bored at work the other day, and decided to dl Cap. Plus fom my gog account to play around in. I don't remember installing it, I think I started and cancelled it, but part of dosbox was on the machine.

Imagine my suprise when my boss posts a notice that he noticed the program and tried to open it. He said it locked up the machine, as well as all usb ports, which meant he could not serve anyone for several hours. He found a trojan in the file, and needless to say I feel terrible. I wonder how this could have happened. Perhaps his attempt to open/uninstall the partial program was a red herring and unrelated to an existing virus? Has gog had problems of this aort?

Although I’ve seen posts from people who encountered AV positives in gog files – eventually they were all false-positives – never heard of anyone who had real infection from a virus that came from gog file.
Possible your boss pissed off seeing a game on a company PC and gives you a warning.

Which trojan did he spot and what protective software triggered the alert (and which specific file was raising the alarm)?

Your boss was probably just screwing with you. Easier than coming off as a hard-ass because he doesn't want you using the PC for your own personal reasons.

Perhaps, but I know him outside work, and while we haven't talked about it yet, what he described would sounds too specific and fantastical to be fictional.

It seems quite strange that anyone in charge of workstations would simply open an unknown file.

People who spend a lot of time with kids tend to use tactics like this, I didn't intend to come off too cynical about it. Have you used the computer to download things in the past?