instance layout doesn't correspond to master layout
Master layout (done with symbol organizer):

Instance sheet layout:

@RaphyRaph, actually I think it does, but whats happening is you have multiple pages of symbols in your library, and all your pages are overlayed on each other in the instance sheet. This is a known issue, one I will solve for in a future update.
I thought that's what it was, so I moved symbols from different pages in non-overlapping positions. It's actually not the case: some of the positioning for symbols corresponds to its parent page positioning, some isn't. Weird..
Interesting... well I will definitely take a look at positioning issues as part of an enhancement to address multiple pages. Hopefully I can get to this soon!