My guess would be that you previously adjusted margin on those pages that don't update automatically.
Reapply Master A to all your pages and it should revive them - be careful though - perhaps do it on a new version using File>Save As
Of the masters where the margins didn't update, two Masters have the same margins as the Master A before the change. When we select the offspring Master for overrides by going to the Master Pages flyout menu, the Remove All Local Overrides option is dimmed out.
There was one Master that did have different margins, and I understand why the update to margins in Master A didn't take in that offspring.
The one common denominator between the two Masters that didn't update is that they are both "unused" in the document at the moment; could that be the reason they don't update with the changes to their parent, Master A?
I just tested the idea that the Master pages that weren't updating weren't updating because they were unused; I created 2 new spreads in the doc using each Master before I changed the Master A, and the two stubborn-child Masters still won't update with the changes made to the Master A margins.
Could this be a bug?
More likely to be document corruption, I think, but might be a bug, perhaps related to the Page tool, which I think may be a bit buggy (there are some problems with Print Booklet reporting incorrectly that pages are not all the same size, and I think those are related tot he Page tool, but it's speculation on my part).
Try exporting the file to .idml and see if things behave better. See Remove minor corruption by exporting
OK, thank you!
I believe exporting to .idml was what worked a couple of months ago when I had trouble with InDesign CS5.5 crashing while working with anchored graphics.