I have the same problem as Alex in the original post, but as there are no funny characters in my URL, I cannot solve it Alex's way.
Username/password are in the DB, I have no meta-refresh stuff (I don't even know what it is), yet, with .htaccess, like Alex, I never get beyond the first page, and I always get:
links found : 1
http://myserver.../subdir/mystart.php
Optimizing tables...
Indexing complete !
Without .htaccess, all generated pages are indexed...
Any fresh ideas on this?