I think you have the objects moved to the wrong layer on the problematic pages when you have placed items.
What you should do, beside the problem, move the page number on a separate layer ON TOP of all layers.
When you place items or write text lock all other layers you don't need at the moment.
Check on each page what happens when you switch the visibility of each layer. There should not be any difference.
If I'm using a Master Page, the layers aren't different on every page...especially the background layer, which is ONLY on the Master Page.
Also, in my initial post, I outline exactly how I laid this piece out. Everything is on the layer it should be on, whether it's on a Master Page or a regular page.
Are you sure that you have not overridden the master page object which could have happen with the text tool ore any other tool accidentaly?