Hi,
I've got sometimes the same problem, but only if I use groups for queueing incoming calls. Are your extensions directly assigned to the PSTN lines?
Regarding you SPA941, I use the same phone. What I found out is, if the phone is permanently ringing (by membership in a queueing group for example where the incoming caller waits for a couple of minutes or caused by the problem you mentioned above), then after a certain time, ringing stops and restarts after a moment again. This is the point, where the next incoming call is counted by the SPA941. (but there is only one call, which simply lasts very long)
This seems to be a behaviour which is specific to the SPA941: I also make softphones participate in the same group - they're continuously ringing without any breaks. (and so counting only 1 incoming call)
regards

Tjareson