I have tried your suggestion by starting on Classic and changing to Polymost in game and I still get the black screen. In meantime I found 2 more bugs that are worth reporting:
1. Start EDuke32 in Polymer mode, then start a new game and change to Classic mode. You will get black screen just as if you started Polymost mode.
2. This one is hard to reproduce and it may take multiple attempts. After I closed EDuke32 with task manager (or guessed where exit was), when I started EDuke32 next time, the Video mode option was empty, supposedly Classic was selected but it didn't show up because by default if I tick Polymer box, only OpenGL mode shows up which is how it should be (at least as of lately, I think in past both modes always showed up regardless of whether Polymer box was ticked or not). However if you leave that video mode option empty (see screenshot of the bug), it seems to start Classic mode with Polymer and you can switch between the 2 modes fine. If you quit game after that (leaving Polymer enabled), you will have OpenGL mode showing up fine at startup. Then it seems to repeat the first bug I mentioned above in this post. Sorry if anyone is confused by what I mean, I tried to explain my best.
Screenshot:
EDIT: Forgot to mention this happens in latest build r8620.