If its commented out its the default which is 1000, and yes this could be causing may more issues and silently hiding them, I've raised the bug here:-On second thought, Is it even possible that this is hitting a ceiling of 1000 field inputs?
There may be more problems if this is the case.
Edit: Just checked and my max_input is still commented out.
http://xenforo.com/community/threads/max_input_vars-errors-silently-hidden.34171/