Just recapping -
The rendering issue with page 1 is GUI/QT only and does not affect topng. I double-checked the glyph positioning issue with page 2 and 3 with the 32-bit binary on your web site too - that should rule out any issue from local customization. Oh, I tried okular too - it uses libpoppler which was derived from xpdf - and okular uses QT too but is not affected as far as page 1 is concerned.
If the Artifex folks are listening - I tried building the latest mupdf from git and git module update --init - that's basically static linking every library from an Artifex tagged preferred/unmodified version . Page 2 and 3 's glyph positioning problem is seen there too (and other viewers on Linux, including acroread 9.5). So I'll file a bug with Artifex at some point.
I guess I'll give windows acrobat reader on wine on Linux at some point, and try mupdf on my android phone too...