I struggled with this issue for a LONG time, so I figured that I'd offer some help. On my site (and I've seen it on many others), I couldn't seem to get the "My Flags", "My Topics" and "Search" links to work unless I was on the main Forum page. It works in Firefox, but not in Internet Explorer. After playing around, I thought this might have something to do with the file names being the same. So...I gave this theory a try...and my solution WORKS. :)
What I did...
1) Copy the /orca/index.php file and paste it in the same folder as search.php, mytopics.php and myflags.php
2) Go to the the database table named TopMenu
3) Find the records for the broken links (Search for Parent=48)
4) Change the appropriate Link fields...
FROM: forum/#action=goto&my_flags=1
TO: forum/myflags.php#action=goto&my_flags=1
FROM: forum/#action=goto&my_threads=1
TO: forum/mytopics.php#action=goto&my_threads=1
FROM: forum/#action=goto&search=1
TO: forum/search.php#action=goto&search=1
Basically...duplicate the index.php with new names, then point the corresponding database records to the custom named files.
I hope that this is helpful to some people. I see that even the Boonex site suffers from this flaw, so it must be a bug (incompatibility with IE).
