Most probably, something / someone messed up with your /var/qmail/queue directory. IMHO the most secure way to solve your problem is to recreate queue directory. So, stop qmail services, back up your qmail installation, change to qmail source tree, run'make setup check' and, eventually, restore your initial backed-up files excluding, of course, the queue directory.
Or you could run queue-fix ( http://www.netmeridian.com/e-huss/queue-fix.tar.gz ) on it, which should fix your problem with a minimum of fuss. At least, it works well for me.