I've media-libs/libjeg-turbo-1.0.90-r1 installed on my system and mupdf works without any problems with it here (~x86). Unfortunatly the ebuild depends on media-libs/jpeg insted of virtual/jpeg so a collision occurs. This simple patch solved the problem for me. Reproducible: Always
Created attachment 254015 [details, diff] patch to make mupdf depends on virtual/jpeg
+ 11 Nov 2010; Samuli Suominen <ssuominen@gentoo.org> mupdf-0.6.ebuild, + mupdf-0.7.ebuild, mupdf-0.7-r1.ebuild: + Use virtual/jpeg wrt #345125 by "Shark".