I cannot reproduce the problem on Scribus 1.4.0.rc5.
1. I created a document "Doc1.sla", created a master page named "Main" on which I placed a colored rectangle on "Background" layer, and some text on "Text" layer above it.
2. Then I created a new document, "Doc2.sla" and imported the "Main" master page from "Doc1.sla". Selecting the "Background" layer and upper rectangle worked as expected, no problems encountered.
Another option would be to create a document with all elements set (master pages, headers/footers, text styles etc.), save it and use it as a template, so you don't have to import anything: just start every chapter from this template, change colors as you see fit, and that's it.
However, if you still have problems, please provide example files which show the issue clearly.