Okay, I know what's going on. This is a bug in a different aspect of Sage, but perhaps it can be fixed on this ticket. On sage.math.washington.edu, the directory /scratch is actually a link, pointing to /mnt/usb1/scratch/. If you have a copy of Sage in a subdirectory of /scratch, then for reasons I don't understand, sometimes Sage thinks SAGE_ROOT is /scratch/... and sometimes it thinks it is /mnt/usb1/scratch/.... This doctest is failing because when the doctest runs, it thinks SAGE_ROOT is /mnt/usb1/scratch/..., while the output from "which gap" starts with /scratch/..., so the first entry in $PATH is the right directory, but with the wrong name. Maybe when sage-env gets run twice, it manages to use /mnt/... both times.
Here's a patch (to the Sage library) which applies os.path.realpath to both the value of SAGE_ROOT and the output from "which gap" (etc.). This fixes the problem for me.
