I set page numbers in the the master page of 2 documents, one of then I get all pages with wrong alignment in comparison of what I intented in the master page. The other document I get some pages with the desired alignment and other pages wrong. Any suggestions?
Have you adjusted page sizes using the page tool?
I haven't used this tool yet, but just tryed now to mess a bit with it and it seems that nothing has changed.
I was not suggesting that you use, merely trying to establish that you had not as the guides in the screen shot are clearly not in the same position as on the master page.
Does this happen in a new file?
I think maybe the first step would be to try and export of the offending file to .idml. See Remove minor corruption by exporting