hi bcogney, and welcome to the forum ! this is indeed the right forum for questions about epub, hopefully you'll get a few more responses soon. sometimes people don't have a chance to reply right away, give them some time

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i can't tell you much about the specific differences between the versions you're using, although i would expect that more recent versions of *any* tool would be more precise and more sophisticated, which could explain some of the differences you're seeing. also, since the epub format is itself still evolving, that could explain some of the differences as newer versions might take into account elements which have only recently been defined in the standard.
when you say "page-map", are you referring to Adobe's page-map ? that should be supported...
personally i use the online checker at
threepress. it will give you a detailed error report which is very helpful. little tip, it sometimes has trouble with filenames containing a comma, so if in doubt, use a very simple (one word) filename for testing purposes.
as for your question about drm, i suspect that that is an entirely separate issue, however in any case, you should always make valid files for compatibility and display reasons.
can i ask why you are concerned about drm ? if you're planning to distribute books with drm, i'd like to suggest you do a bit of research around here first ; drm is generally considered to be inefficient at preventing illicit copies, expensive (a cost which gets passed along to the customer, raising prices overall), and frequently a source of frustration, inconvenience, or unfair limitation / loss of access to *
legitimate customers*. and since the examples of non-drm methods are convincingly successful (see : previous transitions to digital media in the film and music industry who, after years of doggedly clinging to drm and many many stories of legitimate customers losing access to their media because of it, have finally abandoned drm, as well as examples of publishers selling drm-free ebooks like baen books, pan macmillan, or o'reilly). given all that it seems rather pointless to continue using drm !