I'm not aware of any differences in Skinny. But I'm not certain that Witness is actually using Skinny to correlate calls to RTP streams.
I'm sure someone will correct me if I'm wrong - there are many ways to integrate voip monitoring. ;-)
Usually, you'll see voip recording applications using TAPI or perhaps JTAPI to integrate with CCM. These protocols are used to signal to the Recording software which phone or agent is making a call, where the other endpoint is, and UDP/RTP endpoint information, extension to user mapping, etc. Then, based on info from TAPI, the sniffer interface (connected to the SPAN or RSPAN port) can filter out unwanted RTP streams.
JTAPI is not the same between the two versions of CCM you mentioned. And when mismatched, produce some ugly results for the applications using them. TAPI requirements may be different as well (I'm not sure.)
If Witness is saying that you MUST upgrade, that would be consistent with TAPI or JTAPI use. You might want to push them for clarification.
