I'm having the same kinds of problems as the original poster. I took the advice and downloaded the original modules.php and Your Account directory from the distribution and STILL couldn't get the forum admin to automatically load when I logged in as admin on the Nuke side. I DO have a user named admin and an admin named as admin. When I login through admin.php the forum is still looking for a login. If I log out as admin and login through the forum as admin the admin modules don't load.

This might help. When I login as admin through admin.php (and there is no login on the forum) and I try to acces the forum through the forum button in the admin panel, I get the "You are not authorised to administer this board" message. At the bottom of that page is "Powered by phpBB 2.0.3 © 2001 phpBB Group". and the page is generated from "/modules/Forums/admin/index.php". Could it be that the file "index.php" is the wrong file?

As you login as admin (through admin.php), shouldn't you automatically be logged in as admin in the forum when the forum admin login is the same as the nuke admin login? And in what file does this take place?

NO..the Forums use a different read to verify you as an Administrator. It has to do with your user_level setting in the users table.

You can't hack your Superusers user_level setting, thus you MUST be logged in with your USERNAME you created as an Admin for the forums when you installed the Forums in order to access the Forum administration. Loggin in JUST as the Nuke Admin will NOT allow you to access the Forum admin.
No 2 ways about it.

mikem