I just saw the commercial redistribution clause for pdfTK if that's what you're talking about. It does not affect me since this was not a commercial application, but it would seem to me that that clause itself is a violation of the GPL, since pdfTK links to GPL software and it is also a contradiction of a separate place on the site that claims the same software is licensed under the GPLv2. Preventing commercial redistribution is not compatible with the GPL.
Actually mupdf uses AGPL, and so the program I wrote and linked with mupdf is also under AGPL.