1.Are all these calls being metered on one POTS line only .(Your vendor can tell you what phone number the metering is occurring on)
2.Is that line actually connected to your system(ring the phone number and check that it rings into your system.)
3.Get the line checked to ensure there isn't a tail jointed into the cable at the Main frame (I think you call them the closet)-where the cable network enters the building.Could be paralleled to another part of the building and active at another outlet.Could even be tailed off in the street to another address.Stranger things have happened.
4.If all else fails connect an SMDR(System Management Detail Recorder)at the system and it will track and record ALL calls made through the system and what numbers have been dialled from what xtn ,at what time etc.Do this on the quiet so the offender doesn't become aware and ceases.
5.I don't know the system but similar problems occur here if the system has 3 way conference (1 xtn to 2 exch lines)activated,OR has external call transfer activated(call comes into system-at the cost of a local call-and is transferred to another number anywhere) .May only be to another local number BUT may also be international.
You will need an SMDR to chase the xtn user doing this .