Hey MCP,
Sorry to hear what happened. I've used Chocolate Doom and never experienced this. But I just want to say a couple of things.
First: Thousands of people have been using this program. It's an open source project. If it's as horrible as you say and people didn't trust it, they wouldn't use it.
Second: Don't panic when these things happen. From what I can tell, from what you described: the game set the desktop resolution very low because the game itself plays at a low resolution.
When you hit the Windows key, you switched to the desktop. The game probably didn't crash or hang, you just needed to get back to it by hitting Alt-Tab.
By shutting down or restarting, you kept the desktop resolution at that low setting. The way to probably fix it is: when the computer boots up, keep hitting the F8 key. You'll get a menu. Choose "Last Known Good Configuration" and hit Enter.
I can't guarantee it will work. But this should restore your desktop to the way it was, before you reset the computer.
The same exact thing you described would happen with any game that used low resolution, not just Chocolate Doom. If you reset the computer while the resolution is low, your desktop could get stuck that way.
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