We have the same issue but it comes through CAM correctly.
So is the set back of your end cap geometry achieved using a negative value in a dimension? Something like Length in CID 31?
I stumbled across an old post that Andy responded to. I don't have it handy right now, but it was something like 2006 old and the advice was to use the "node" of a connector to offset it either direction from the point of connection.
My suspicion is that Autodesk is only getting this question from places that used actual geometric dimension exploits, unknowingly, to achieve it.
Anyway, if you go into your connectors, select the recessed end cap connector, hit "Breakpoints" and put the proper negative adjustment in the C node, your end caps should set back again.
You can then probably set the ITM length/turnover dimension to 0, just so you don't have a useless negative dimension laying around.