Kerbal Space Program

I am having trouble saving the game and recovering my vessel when I perform rendezvous missions. It seems to be related to the RCS thrusters on the 3 seat Apollo style command pod (I don't remember the name of it). The steps it takes to replicate this mission are included below:

1. Launch a vessel to orbit with two separate ships attached: a lander and a mothership (the mothership must include a 3 seat Apollo style command pod).

2. Separate the lander from the mothership when in orbit of a celestial body.

3. Either land on the celestial body with the lander or go completely out of sight of the mothership.

4. Return to the mothership in orbit.

5. RCS thrusters on the command pod of the mothership look like they are firing, but it is not making any change in the orbit of the spacecraft. Disabling these thrusters will not fix it.

6. While trying to save the game, it will not respond as if I am not doing anything at all.

7. Once returning to Kerbin, the "Recover Vessel" button and the "Return to Space Center" Button will not work. The only way to return from the flight screen is to revert the flight. Note that the command pod thrusters on the mothership are still looking like they are firing.

I will add screenshots of this happening if needed.

Mods installed: BetterTimeWarpContinued, Toolbar Control, Click Through Blocker, and Kerbal Engineer Redux