The problems was a compiled qmail-pop3d+vpopmail.c.diff patch
I found it by comparing the strace output of the test server and the
production server and noticing a systemcall to getpid which wasn't
happening on the production server.
I grepped for it in the sources of qmail and noticed a patch was
applied. I reversed the patch (in this case for pop3 traffic logging)
This time, everything is working as it should.
Thanks to all that helped isolating this problem