Hello again!
Thanks to Matthias's genius, I now have most Atari 2600 games working flawlessly once more. However, they are a little slow now - it seems to be about one second per kilobyte (varying slightly depending on which bankswitching method is used), with most Atari games being from 2kB to 16kB. This isn't too much of an issue though, in my opinion. Basically the problem was that for some electronics reasons I don't understand, changing every bit at once on the address buses of Atari games was causing a power drain causing the processor to freeze. This affected some people's units worse than others due to natural differences in the tolerances of the components. The fix is to only write to the port bit-by-bit.
However, I've run across another interesting issue that isn't any fault of the Retrode hardware or software that is interesting.
Atari 2600 game ROMs have no headers, and there is also no header in the file. However, Atari 2600 games sometimes have RAM on the cartridge and sometimes don't.
So, emulators decide whether or not to emulate RAM based on the checksum of the game (among a few other things as far as I can tell).
However, the checksum of the game includes the RAM. RAM is not always going to be the same.
You can see where this is going.
Games dumped by the Retrode, through no fault of the Retrode or its firmware, have a different RAM each time. So, the emulators don't always detect it as having RAM and you must specify manually that it does. This only works normally because the emulators have checksums of most/all of the ROMs on the internet; even for those there doesn't seem to be a convention for what to fill the RAM with (some have it as 0s but others have again random bytes). But obviously stuff from a Retrode isn't going to be the same as stuff from the internet, so the checksums won't match.
I suppose the only real way around this would be to moan at emulator authors to not include the RAM in the checksums. However, this would still have problems for previously undumped games (which are more common than you think; most games where the PAL versions are different have no PAL dumps online).
Thoughts?