I have been through this, yes. Innovus (and Encounter before that) has lots of buggy behaviors when you use powerDomains.
Usually the top powerDomain has interaction with the others and causes the tool to get confused. I have a chip being taped out right now where I did filler insertion BY HAND because of this.
The way you commit the power intent also matters, I have found out. Loading libraries with MMMC and having power domain in UPF/CPF makes it even crazier.
Bottomline is I don't know how to help you, but you are not alone. This functionality has been broken for years.