R.Belmont, thanks for explaining, makes sense now why it wasn't working the way I expected. I did convert my sysutils1.3 dsk to po, and it also did not work, so had me confused a bit.

Looks like there are a couple of other A3 SOS boot sectors that it might be good to add in support for. One looks like an older Apple one, and one is used on the BOS operating system disks written by Bob Consorti. This second one looks like it supports the 512k ram option. Here is a link to the disk images for these:

That disk image that did not work was just my attempt at putting atomic-defense back together from my disassembled source. The boot sector for it uses the block io inbuilt into the apple3 firmware, so it was easier to just use a prodos ordered disk to just add the code parts together to make an image. I don't think there is much point adding this one in at the moment, i'll just convert to dsk and work with that for now.

And still on Atomic-defense, I worked out why the text screen disappears during the game play on some machines. The Alpha Lock key is checked by the code! If the key is down, then the text displaying the score is kept at the top. If the key is released, then the code times 240 VBL periods (4 seconds) and then removes the text from the top. It Mame it works ok once you toggle it in the game, although Mame does not seem to carry in the current state of the capslock key into the emulator on startup.