Kdgarris, Great looking and playing game!!!! You wrote: "However, there is still a serious bug in the display of the score where digits are repeated after 1,000 points. I don't yet know a way to work around this issue."
For what it's worth, I see this with all bB developed games that use the 6 digit score, mine included. The emulator with the Flashback Portable has soooo many issues! Anyway I asked Nukey Shay to take a peek at some of my games and he fixed the score display bug. He disassembled by .bin and switched a thing or two and posted the corrected versions on the flashback compatibility tread. Sadly, I don't think it can be fixed in bB directly as his fix was working around a bug in the portable emulator. You'll probably drive yourself crazy looking into this but here is a link to his comments when he created the fixed binaries that work with the portable.
related comment "Score fixed by hitting RESP's 2 cycles earlier, and shifting both HM's 2 pixels left."
If you ever find a way to correct this, probably possible in the bB score code somewhere in the include\std_kernel.asm, score_graphics.asm or the pf_drawing.asm files please post it!