Makes sense, I did notice how the FDAI wasn't exactly at 90 degrees pitch after P01.
The FDAI would have shown 90°, because that is the pitch angle that the CMC torqued the IMU to for launch, not the actual pitch angle of the launch vehicle. If you take a look at the HUD view outside of the cockpit (press F8 twice) then you will notice that the Saturn IB points to about 88° pitch and 1° yaw. That will be enough of a misalignment to cause the insertion issues.
As for the CMC issue, my saved scenarios seem to work fine, as all of them are at least at T-30min. It's the T-4h scenarios that come with the latest NASSP release that have this issue. The old scenario, Apollo 7 Virtual AGC LVDC++ MCC - Launch.scn, has no such issue even when used on the newer release.
I am a bit confused which scenarios you use with which NASSP version. Are you using the latest scenarios from the NASSP 8.0 Alpha releases with the Orbiter 2010 branch? Or did you try it with the NASSP 7.0 release version? The NASSP 7.0 release and the Orbiter 2010 branch are not the same thing.
I tried the Orbiter 2010 branch, but the T-4h scenarios that come with it work perfectly fine. The Orbiter 2010 branch is a bit of an experimental branch which hasn't been updated in a while. It was only created so we could test launches, when that wasn't possible yet at the time in NASSP 8.0 due to Orbiter 2016 changes. I might give it another update, so that all the latest changes for NASSP 8.0 can be used in Orbiter 2010.
Is it safe to use the old scenario with the newer NASSP release, or have there been significant changes made to NASSP between the two releases such that I may encounter other issues down the road?
In general, yes. You can use older scenarios. If you encounter a scenario with a permanent STBY light on then the AGC save state is broken, due to the saving format changes I mentioned. It is possible to fix that by editing the scenario, but it is a bit of a hassle. If your RCS seems to be broken in an on-orbit scenario then you have to activate the "RCS Enable/Disable" relays again. These simulated relays have been moved internally in NASSP, so they can appear as off in older scenarios. All you have to do is close the SECS circuit breakers on panel 8 and then switch RCS CMD to On on panel 2. For the CSM these are usually the only issues in older scenarios.
All the Apollo 7 and 8 scenarios that you can find under "Project Apollo - NASSP\Apollo - Historical Missions" have been mostly updated with the NASSP changes. So at least the CMC problems shouldn't happen in those. If your own older scenarios won't work, then you could try one of these scenarios instead of flying a whole mission from scratch again.