Some platforms/perl versions don't support flock. Mod_perl will give you trouble with all those global variables and unlocalized handles - each connection will think it has the lock (I withdraw the "lexical" word). Your locking code will work on the right system under ideal conditions, but there are many things that can fail.

You haven't shown your error logs and you don't say what platform, perl version, whether threading is in use, or whether different connections have a new environment.

My advice was to simplify the locking and isolate variables' scope.