Comment 7 for bug 336684

Something I can see right away (not sure whether this might have caused the problem or not) is that you have double slashes in your filenames like /tmp/scan//out1.tiff.

Other than that, it mysteriously fails right after

ModulesInit -> RSTR_Init -> p2_msk_init -> MSKInit("rec4inc.dat")

but it seems to have read this file, so obviously it can find it somehow. Sorry, but I am not of much help here :(

I find it strange that it only fails if evoked by the daemon with root privileges. Did you try to evoke it manually using sudo as your current user and as root on the same file and compare the differences between strace logs?