I was experiencing this problem in a SQL window. I would connect to a database, execute some queries, let it sit idle for a while, come back and try to re-execute the last query. An alert would pop up saying "ORA-03113: end-of-file on communication channel" and I would then have to manually reconnect.
Ofcourse, after reading your reply I tried to recreate the problem, and it mysteriously vanished.
I'll be keeping an eye out though...