Yeah I am getting the same thing. So I think the RTCC MFD wasn't set up quite right, missing one minor step. On the configuration page of the MFD next to the TYP button it says "CSM". That means some parts of the RTCC MFD treat the vehicle configuration as CSM alone. If you press the TYP button once it will switch to "CSM/LM docked". That is what you want for the next while.
And I believe this has an effect on the SPS trim angles the Maneuver PAD calculates. So it calculated the angles for the CSM alone, which are quite different. Maybe for a longer burn the TVC recovers, but for a short burn you will get residuals. If I use 0.1x time acceleration I have enough time in your T-2min scenario to exit out of P40 (V37E 00E), then start V48 and enter the correct trim angles (about +0.96° for pitch and -0.23° for yaw). And then go back to P40. With that I get a good burn.
A few other minor things I noticed in your scenario. Not all pitch and yaw thrusters are enabled (Auto RCS Select). That might be a configuration for PTC or so, but normally you want all pitch and yaw thrusters enabled, or else doing an attitude maneuver causes a translation, alterating your trajectory slightly. For roll you usually have either A/C or B/D quads enabled, but during a burn you often want all thrusters on. And you probably didn't care for the SCS in this case, but I think it was set to Att 1/Rate 2 (which is the attitude hold mode) at a different attitude than the burn attitude. On FDAI 2 you can see the error needles have a large deflection. If you switch to the SCS in that T-2min scenario you would get a lot of RCS firing. Just put the three BMAG switches to Rate 2 and then back to Att 1/Rate 2 to hold the current attitude.