I also have the same Problem.
While i can start Batocera from my stick with it, as soon as i install it on the internal eMMC storage (32gb) it does the same what AMK discribed. I tried turing off Fastboot, but apparently that is not possible (only options are: minimal, thorough and Auto).
And now i don’t know what to do, because apparently i cannot install it on the internal storage anymore (it does not show when i load up batocera from the stick).