I had similar issues -
to bypass any cache issues
I renamed the xar file, saved to a new folder in my PC
and uploaded to a dummy folder on the server
hence was NO previous cache
and I STILL had issues
ie looks ok on preview but not in the browser or when uploaded
I had done the same as you - many copies/paste from other pagers or other xar, etc
seems my issues were layer related
eg I would paste a photo or text - and it would not appear
so I would paste it again
then find it and arrange? move to 'top layer' and would appear
then slide into a location on the page I wanted
but I think the underlying version would still cause formatting issues
most often trying to have a photo push the surrounding text - it would be all goofy
^^ this was all before I became better at understanding layers (still learning)
*eg paster broad, page, mouseOff moueseOver etc
as I got better (still a rookie here) - I found duplicate items everywhere in the wrong layers

I also found many empty text areas
seams as when you make a text area or text line
and then click elsewhere (as in done making text in that location)
it makes a new text area where you clicked and that was also upsetting the formatting/item spacing

hope the above helps
sorry if it seems rambling - but it is as I recalled
(I am just an occasional user)