I can't think what is causing that. It sounds as if you are doing everything right.
You are probably the first other person to run my port, so it has not been tested much, but several of the games in the Startdot collection worked for me. The Blackice I/II version was much more widely used.
I changed the clock speed for VGA from 25MHz to 32MHz to run on the Blackice Mx, and was surprised that it worked so easily. But you problem sounds like more than a problem with VGA synchronisation.
I will let you know if I think of anything that might be causing the problem. A problem with SDRAM is possible but I am not sure that matches your synptoms.
I haven't used the Blackice Mx board for a while, as I am now working mainly on the Ulx3s ECP5 board.
I have the Jupiter Ace running on the Ulx3s board, and am looking at ways to load programs for it, such as using Ace snaphots loaded from the SD card.
I do plan to try to get the Acorn Atom and perhaps hoglet's BBC Micro port working on the Ulx3s. If I get any ideas when I do that, I will let you know. It may not be for a while.
I also have the start of a ZX80/81 port for the Ulx3s board, which would probably also run on the Blackice Mx. But that has problems with screen corrupton, too.
Have you tried my NES port? I used that more than the Acorn atom port. That also needs roms loaded into flash. That has also been ported to the Ulx3s board by @ironsteel.
Ulx3s boards are available at https://www.crowdsupply.com/radiona/ulx3s/updates/ready-for-crowdfunding
The main thing I worked on with the Ulx3s is getting SaxonSoc Linux working. That board run other retro ports including the Amiga, and MS-DOS.