htaccess weirdness

[eluser]GridWave[/eluser]
[quote author="Daniel Moore" date="1244847531"]
#1, are you able to surf all your CodeIgniter paths without error?
[/quote]
Yes
[quote author="Daniel Moore" date="1244847531"]
#2, is it only when you access seoTools with the "Require valid-user" that you have the trouble?
[/quote]
I only have trouble when I get to the first page after authentication and clicking on a link to do something else.
[quote author="Daniel Moore" date="1244847531"]
#3, is your directory structure as follows? (If not, then please clarify.)

Code:

webroot
|-.htaccess
|-index.php
|-system
|-seoTools
  |-.htaccess

[/quote]
That is correct and then the seoTools has a similar file structure to system (if that makes a difference).
[quote author="Daniel Moore" date="1244847531"]
#4, have you considered using something other than Apache's authentication method? Perhaps coding your application for authentication?
[/quote]
I was asked to get this done quickly and using that authentication method seemed to be a quick and dirty way to get around login/password. (Read: lazyiness)

As I mentioned before though, this was working before the htaccess file was deleted.