** Using WeBWorK **

I vaguely recall situations where students type an answer that WeBWorK doesn't understand (e.g. using extended characters, or with a syntax error).  In these cases I believe I've seen it mark the answer wrong, but have trouble writing the answer to the past answers table.  I would think something like this would be more likely than a database problem which only intermittently affects one table.

Have you checked the apache error logs?  If WeBWorK is having trouble writing to the database then I would expect there to be errors somewhere.