Yet again I can't load your scenario because the S-IVB section of the scenario is incomplete. Are you sure you didn't delete anything there? Can you tell me exactly which version of NASSP you are using? Orbiter 2016 or Orbiter Beta (with revision number) and the exact NASSP build number. I can of course delete the S-IVB from the scenario as I did in your PDI scenario, but it just doesn't make sense to me. You are clearly using NASSP 8, I can see that from the other scenario parameters. But all the S-IVB is saving is the default Orbiter parameters, none of the vessel specific parameters, no LVDC, no EDS, nothing. Why does it do that???? Is the S-IVB module auto build broken???
Apart from that your scenario doesn't look that bad. The AGC seems to be locked up somewhat in the coasting integration routine. You can actually watch that happen by monitoring V16 N38, whichs shows the current GET of the state vector that is being processed. When I do that in your scenario it first shows a GET of about 109h, 13 hours in the past. Not sure why it does that, usually it will automatically update the state vector every once in a while. Did you have the CMC in standby or turned off for some time? Not doing V37E00E for a long time might also cause this, not sure. Eventually N38 would reach the present time and the AGC probably would work fine then, although that can take quite a long time. The AGC is slow.
In any case, a V96 stops the processing and if I then uplink new SVs with the PAMFD it all seems fine. Careful though, don't uplink a LM state vector, the LM is still on the surface and that can be a bit unhealthy for the AGC
If you just wanted to fix the AGC then uplink a "Columbia" state vector to the LM slot. Alternatively, the MCC also wants to uplink state vectors which works fine after the V96. And that LM state vector is a useful one.
Now, the state vectors that the MCC uplinks kind of cause the opposite issue. As the Checklist MFD says those CSM and LM state vectors are time tagged at insertion + 18 minutes. So they are 2+ hours in the future. So if the AGC then needs to find a present GET state vector it has to do a bunch of processing again, although not as much as the issue before. The mission documentation often states the time tag for a state vector, but it does cause some issues where the AGC has to do lengthy processing at critical times, especially for Apollo 10. So we are still debating if it is a good idea to uplink state vectors that far into the future, or if it wasn't better to let the MCC uplink state vectors at the present GET all the time. Maybe we are misunderstanding something about those SV time tags.
Anyway, I think all in all your CMC is in good shape. Just do the V96, let the MCC uplink state vectors and you should be fine.