Not sure, but I guess it uses ram in C000-FFFF were MyBIOS runs.....
Those games will never work under the MyBIOS that run from Flash/Ram.
You need a MyBIOS in ROM that replaces your internal Atari-OS.
But anyhow, best is to store the disks in images.
Be aware you must copy them in the correct sequence and optional a empty DOS2.5 disk in the last slot.
When you need to insert disk #2, just press SHIFT+CONTROL+2
When you want to save, and the empty disk is in the 5th slot
press SHIFT+CONTROL+U (to unprotect the image)
Note: all images are protected on load and swap.
The user must unprotect them before writing.
Because there are some games out-there simply format the image when it's not write protected
Kind of copy protection.....