There's a possibility it's being overwritten, since you're generating your row ids by hand. You could lock the table while you're doing the insert, which is usually a bad idea. You could wrap the whole transaction in a transaction, if you're using MySQL 4.x (people who want to complain and bandy about the phrase "ACID", go waste your life in Slashdot discussions; you guys bore me, at best).

I'd rather make the id column AUTO_INCREMENT, though, in which case you don't have to insert anything and it generates a unique ID automatically.

Other possibilities are that your uploaded file is hitting a resource limit or that your server disallows multiple CGI programs to run simultaneously. This really feels like a concurrency issue, though.