Just to bump this. I have just tried updating my version of pligg to 7.2 and I get the same problem. I am installin into a subdir "/data" and when I click on, well anything.. I get a 404 Error.
my site is here
www.ob3y.com/data
for example when I try to select "Search for Stories" It tries to take to to this url
http://www.ob3y.com/data/shakeit/
and informs me that it can't find the page (For good reason, the /data/shakeit/ dir doesn't exist! I've tried updating my .htaccess file with some of the ones i've seen floating around, but that didn't seem to help. When I did the upgrade, I ran but the DB upgrade, with success, and also the upgrade_link_url.php link, and that seemed to work fine.
If anyone has any idea, I'd appreachate it!
-Pax