Unfortunately we never found the cause. After deploying a new version of the app the scheduled events worked again.
I'm not sure, i bit of a long shot from my side, but isn't a scheduled event run in system context, so there is no currentuser available? This might be an issue for executemicroflowasuser.
Did you upgrade? If I recall correctly something changed in some version between Mendix 7 and 8 within the Mendix Java API concerning using system context for running microflows from Java.
Mendix suggested this might be caused by database corruption and it might need cleaning. Created a backup and cleared the environment. Redeployed and restored the database. Unfortunately the scheduled events still fail.