There is not much I can add. This problem seems inconsistent, I will assemble a mechanism in what I consider to be the standard way. I will then place a motor on one of the motion axis and assign a profile to the motor. When I "run" the analysis one of the moving parts will remain stationary and all other parts including the ground body will move on the screen. This is repeated in the play back mode. If I do a body check the system will indicate the bodies correctly. The analysis appears correct, but the system picks the wrong item to remain stationary. Often if I edit the design in some minor way it will then "run" in the way I expect.
I have been unable to figure out what if anything that I am doing wrong.
when i face this problem in gearing i just switch to default views front, top...etc.after that grd gear remains stationary,and moving rotates about it. might this help you in your problem.
Don't know what exactly is happening. However, I normally follow this practice,
The ground body is the FIRST part in the assembly and is assembled to Default constraints or is FULLY constrained.
All other members of the mechanism are then assembled to the Ground member with mechanism constraint.
I have seen this to, but in my case I think it is related to saving a higher level assembly.
Example: my sub assembly has the grounded component on the right hand side (which is real world) and all of my components build on to it moving to the left.
The toplevel assembly has its grounded component on the left hand side of the assembly (these toplevel components do not move at this level) and my sub assembly is assembled to this toplevel assembly to the right.
Having grounds on both sides of the assembly is not ideal or normally wanted in the assembly but using mechanism general constraints allows this to work. (not how I would want to build the assembly).
If the toplevel and my sub assemblies are saved at the same time after draging or moving the moving parts. I think this is where Pro/E gets confused and flips the grounded parts.
The only way I have found to fix this is to insert at the first component, redefined it and all components after it.
Hoping someone else has a better fix.