Thank you for your post.
These intermittent problems are difficult to diagnose.
Check to make sure you don't have a script that deletes a record in table 1 (as this would delete records in table 2). Also, check your relationship graph to see if there are any other relationships to table 1 that might include automatically deleting related records. Also, make sure none of the clients delete a record in table 1.
Any other information you can provide may be helpful.