Hey @Hallie, thanks for the detailed description of your issue, this helps narrow down things by a lot.
The error in the Script Editor seems like an issue with our code, I’ll patch that up on Monday. It won’t affect the recorded result, and would simply leave it as “Override” which is the default.
For the popping, the first step in debugging this would be to try Ragdoll → Utilities → Extract Simulation. This will record the simulation onto a new set of Maya joints you can use to compare with. These should match the simulation, and is a good first step to see where the problem lies.
From there, try the option inside of the Extract Simulation option UI to “Attach”. This will perform the next step in the recording process, of constraining your controls onto those extracted joints. I expect this is where you will start to see your popping problems. And it’s here you can have look at any of your popping controls to see what the constraint for that control is doing.