Yes this is a SDX issue.
I have talked to the SDX-guys about the dual-setup but did not get a commitment
You find the SDX-image in the first 256k of the 512k MyBIOSFS.ROM file.
As you know, the altirra image is a reverse image of all 8k blocks.
After moddig the SDX-rom with the spartados tool:
You have to change the start-up-bank in the first bank of the 8k SDX image.
Found at $1FF1 from $00 to $20.
This can easily be done with a hex-editor of some kind.
(Bank $20 is the start-up bank of MyBIOS-SIDE)
Alternative and you can check that for me
Put the switch in SIDE and powerup, wait for menu, it should appear.
Then switch back to SDX.