Oki, there might be other solutions but for now, after searching the interwebs, I found that the problem disappears if I prepend my code with a myapp.db.session.commit(). I guess, somewhere a transaction was waiting to be committed.
def setUp(self):
# other stuff...
myapp.db.session.commit() #<--- solution!
myapp.db.drop_all()
myapp.db.create_all()
# db creation...