I am having the same problem: can’t save sequences, external private object, MovieScene. 
my post Did you ever find a solution?
I also am using Control Rigs, and the problem does appear when the same control rig is used (and keyed) in two or three different sequences. But, other scenes have control rigs used in multiple sequences without a problem. (Also, those are different control rigs…)
Hmm… this gives me something to test. I’m curious if you got anywhere in your troubleshooting.