well i think it might have something to do with the messy thing about html where you can only save it as text (ie you can't save an html page with a lot of pictures as a sihgle file, unless you use IE that is...)
shame though that pdf actually has no universal standard. i haven't had much problem with pdfs but i have heard that the spec changes with every new version of acrobat, to the point of incompatibility, which irritates me.