I have document DA with master page MB that is based on master page MA. In another document DB I load the master pages from DA. The master page MB is shifted down, the items shifted down are the ones inherited from MA and not the ones on master page MB. If in DB I click on mast page MB options and I set to be based on none, click ok, then set to be based on master page MA then it's everything ok...
It might be because when it loads/syncs master pages it loads the master page MB before MA. I think is this because only happens in one document and I cannot reproduce the error in another, even if I copy paste everything from mine to a new one. Also updated the bleeds and the error cannot be reproducible.
Also if I create another master page MC that inherit from MA the same error happens, so the problem is in the master page MA and I don't know what to do. I cannot just create another master because it will not keep in sync my other documents in the book.
If the error is only in one document and it doesn't reproduce when you use the same procedure in a different one, the problem is most likely to be with that one document. Use 'File > Save As' and select IDML as the type (versions earlier than CS6, use 'File > Export' and select IDML).
Open the saved IDML file, which will create a new InDesign document that is identical in appearance to the original, but without any corruption or "cruft" that may have built up in the original file as it was repeatedly edited and saved. Its file size also be smaller than the original -- possibly much smaller. Use this instead of your original.
[Later Edit] Another possibility is that you have changed margin settings and/or page size from one document to the next, and possibly have
Enable Layout Adjustment turned on. That's a combination that probably would create the problem you are seeing. My usual workflow with books is to create a master template for the book, and create all chapter documents from the master template. This can be as simple as a blank document with the main Master Page and a Chapter Opener master plus a base set of Paragraph and Character styles, saved as an INDT.