I've just upgraded from 2.83 to 2.91. Everything went smoothly but the CSS style sheets failed to load. Looking at the page source showed that RP thought that the style sheets were in site_root/cgi-system/php.cgi/stylesheets. Same for all the images . . .
Digging around in index.php and also pp-inc.php it seems that the problem is down to $Globals['maindir'] not being set on my machine. I'm not sure if this is common or just a quirk of my system but the work around is to add the line:
around line 111 of pp-inc.php.
Everything works then