This sounds very odd - when you press SELECT+PLAY to enter disk mode, you're entering Apple's "emergency disk mode" which is safely stored in (flash) ROM. A Rockbox installation doesn't touch this, so shouldn't stop that from working.
When you reset your ipod, code is run in the following order:
Apple Bootloader (in flash ROM)
Rockbox Bootloader (on disk)
Rockbox (on disk)
"SELECT+PLAY" is interpreted by the Apple Bootloader, which would make the order in that case:
Apple Bootloader (in flash ROM)
Apple Disk Mode (in flash ROM)
If I was you, I would restore my ipod (using itunes) which should re-install the Apple bootloader/disk mode in flash, and see if SELECT+PLAY works then.
If it does, then re-install Rockbox, and see if it still works then. If not, then I'm not sure what to suggest...