Try updating your graphics drivers. What error does Windows give you? Also, are you running 40d or 40d11? It's hard to help you without these kinds of details.
I don't know what you mean by either of those modes, but due to needing to do... well a lot of work to get a slave drive running recently, everything is updated. I even checked for new graphic drivers just now, and I am fully updated. I already tried deleting the folder and installing from a different mirror, the same one that was successful for my laptop actually, (though oddly, the icon for the .exe file is different between the two.)
I have run it in full screen and windowed mode as I mentioned in the first post. I may have been a bit vague about that. One causes a black flash, the other causes nothing. After that with either I get a windows error. No number attached or anything.
One thing to note is that I have to approve running the file. Windows seems to think all the related files are dangerous. I think this was true of Vista though, since I had to do the same thing there, (I don't have that annoying setting where you have to approve everything run with Vista, so this was unusual,) but it still ran after I approved it.
Unrelated: Trust me, I know how weird it can get with graphics drivers and non-graphics games. I play a mud most of the time, and my PSU has been too weak to support my system since I installed my slave drive. The first thing that went was my video card so I was left with onboard. Apparently you need top of the line graphics for scrolling text... >.< (Note: this hasn't interfered with DF, usually the comp works normally, sometimes it just has a tantrum.)