Just as a test, can you try setting $g_short_path = '/tracker/' in your config_inc.php and see if this still occurs? I believe this is related to bugs 0009266 and 0009043 because of the way that Mantis attempts to determine a relative URL to work with external applications (like wikis) that use the Mantis header/footer calls. Unfortunately, with the way it's currently implemented, and URL rewriting by Apache, or filesystem symlinking on *nix hosts, can break this detection method, in which case setting $g_short_path manually will at least override the (incorrect) detected value.

This did not seem to have any effect - other URLs in the tracker seem to still work fine (or at least I haven't noticed any incorrect ones), but the URL for updating plugin settings still seems identically wrong.

Just set $g_short_path = '/tracker/' to $g_short_path = "";

Then it works as it should

Nope, then I get:

SYSTEM WARNING: strpos() [function.strpos]: Empty delimiter

In the "Status" column of my view_all_bug_page.

EDIT: This was due to construction of the URL to the assigned-to user.

Thanks for the info Blue Ninja. Found a missing parameter in the core plugin that was generating a relative URL for the redirect when it shoudn't have, and that was getting tacked onto an absolute url...

Fixed in SVN trunk, r5368.

Ahh, interesting - works for that plugin, but not the FAQ plugin still. I figured it was common code for all plugins - I'll post a link here in Bug 0009261 for him to take care of there. Thanks!