I had the problem that on my Android device only the Agenda View showed up after syncing. Debugging the issue it turned out not to be a problem with mobileorg-android but in the ELisp code: basically no SHAs where computed for the other files, hence they were not included in checksums.dat and for this reason not available in the Android app.
 
Details and workaround are described on the issue page https://github.com/matburt/mobileorg-android/issues/246#issuecomment-7204576 of the mobileorg-android github project.

Cheers,
Mathias