We found that to use mod_perl, we had to change "gbrowse root", which is fine, but it wasn't obvious that this would "break" the "Help" links. The problem was resolved by changing the value of GBROWSE_HELP in the gbrowse Perl script.
Maybe there is a way to reset GBROWSE_HELP by changing something in the .conf configuration files, but if there is, it's not easy to find. In any case, I think it would be preferable if GBrowse paid attention to "gbrowse root" when looking for the help files.
LSIIG, Princeton University