In an offending file, what have you on:
View > Reference Pages
page: MasterPageMaps
And if it doesn't exist, that means you've never run:
Format > Page Layout > Apply Master Pages
(which creates that page, and on subsequent invocations, applies any specified mapping)
The UnstructMasterPageMaps table needs to be populated with the MP assignments you desire.
In any case, on fail left pages, what says:
Format > Page Layout > Master Page Usage
