errata note: When one of the two the pattern table pages is selected, the wrong tile may be fetched by the PPU at the exact moment that the CPU writes to the mapper register. To avoid this, you must not write to the mapper during rendering. The other pattern table page is not affected.
I created this rumor, and I can finally put it to bed. The work-around is dead simple - don't use absolute indexed addressing mode to write to the register. E.g., do STA $5000 instead of STA $5000,X. That was easy.
Why this happens, is because the 6502 accesses memory on every cycle. LDA ABS,X takes 4 cycles, 5 if a page boundary is crossed. But STA ABS,X always takes 5 cycles. By the time it hits cycle 4, it's already read the opcode and is working on fixing up the high byte of the address (for page boundary cross) but it's still going to access memory. You wouldn't want it to do a write, because the address hasn't been fixed up yet. So it does a read, and discards it. The mapper register is sensitive to reads, so the register value becomes the open-bus value (the high byte of the address) for one CPU cycle.
That explains why there have been zero complaints about it. It was my testing method that failed. I've hacked a few UNROM games and simply changed the mapper address, but not the opcode, so the glitch manifests. It seemed weird that I didn't see it happening in my own programs. Mystery solved.
So now instead of a bug, we have a strange new feature. It could be used like the PPU 'monochrome bit' to benchmark your CPU usage. Or you could write to it in an idle loop to create a glitchy screen noise effect. It can affect the attribute table as well, which can get pretty colorful. Just do a STA $5000,X if you want to try it.
GTROM - $9.25 each, if you're looking for a cheap simple mapper. $35+shipping for a devkit.
Here's what the mapper write looks like (74HC377).
1(yellow) is register clock (inverted M2)
2(cyan) is register enable !(PRGCE & A12 & A14)
3(magenta) is data output (supposed to be low)
first image is normal write - STA $5000
second image is glitched write - STA $5000,X