I’m having the same problem as “emuexplosion”. Mine was working, before ... I use TortoiseSVN Update and I’m updated to the latest build, 672 (presumably CI 1.5.4).
Now, nothing but the default Index() works. I can’t even call my test() functions. These test functions are in my default controller class file, as is the Index(); so, it’s getting to the default controller (specified by ... RewriteBase /CodeIgniter/ ) ok.
My application calculates sidebar links, which look correct; but, it won’t route to them.
I noticed that when I follow the RewriteRule on the (User Guide URLs page, it renders the webRoot, rather than CodeIgniter, which I’ve located in a directory right below the webRoot e.g. /htdocs/CodeIgniter/
The 1.5.4 User Guide says to use:
RewriteRule ^(.*)$ /index.php/$1 [L]
but, it will only render the XAMPP start page.
If I delete the slash before index.php, like this:
RewriteRule ^(.*)$ index.php/$1 [L]
it goes to my default controller index() and page, just like “emuexplosion” is experiencing.
Here’s the .htaccess, I’m using ...
RewriteEngine On
RewriteBase directory must be set, relative to /htdocs/ webRoot
RewriteBase /CodeIgniter/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ index.php/$1 [L]
I, too, am going nuts, since I can’t even get an echo to work - to test my way out of it. 
Thanks, in advance, for whatever guidance and insights ...