Hi Mike,
I consulted with the development team on each of the two duplicate CDR cases you mentioned, and here is our analysis:
INTER_COMPANY DIRECTDIAL
Our theory is that somehow the call may be directed to both engine servers separately.  To further anaylze:
1.    Can you send logs from both the engine and admin servers. We want logs from when this happened so if logs from the record you show below have already rolled-over, can you send us logs from a more recent occurrence of this. You can send us logs through the usual channel.
2.    Is this observed only for the case where call was rejected with reason 21?
3.    Is this observed only for calls from/to a specific endpoint.
4.    Is this observed only for calls from/to a particular route.
INTRA_COMPANY DIRECTDIAL
These CDRs are imported from the CUCM as part of a background periodic task.  Our theory is that the CUCM is sending duplicates and CTX is not detecting them as duplicates, perhaps because of some subtle difference in the data received from CUCM that is not exposed in the CDR API.  Please send us admin server logs for around that time period, and we can further diagnose.
Thanks
- John