Based on Master Pages

I'm having a weird issue with'based on x' master pages, when I set my B master to 'based on A master' The pages are not identical, the right hand footer moves along with the vertical guides on that page (see pictures below). I cannot understand why this would be, both pages are exactly the same size, my only theory is that I used liquid layout earlier on when I was creating a template, could this still somehow be affecting the pages now? Enable layout adjustment is turned off if that's in any way relevant?