You cannot be a duke with an estate, and not also be a region lord. There has to be an unbroken chain, top to bottom:
Liege > Vassal
-------------------------
Ruler > Duke > Lord > Estate
You cannot occupy two positions in that chain with someone else in between. I.e. You can't be both someone's liege and vassal. If this situation happens, then it is a bug. It should be resolved by the cleanup script, by booting you from positions, starting from the bottom up, until the discrepancy is resolved.