SEF in Mambo with theGillis patch -bad login/slideshow links

I have Mambo 4.5.2 installed and gallery 1.5 set up. It works fine both intergrated into mambo and also outside, as in you can view all pictures and albums (as far as I have tested anyway).

I have used the patch provided by theGillis to create proper SEFs (Using Xaneon's Extensions beta 2) and so far so good. http://www.thegillis.net/programming_papers/php/mambo,_xaneon,_and_gallery_sef_extension.html

The problem is the slideshow and login links at the top of the page don't actually direct it the the login popup or slideshow link.

Eg:
Integrated gallery into Mambo - clicking slideshow doesn't work:
[url]www.robertliu.com/photos/[/url]

Stand alone gallery- clicking slideshow or login doesn't load anything except the same page:
[url]www.robertliu.com/gallery/[/url]

I noticed the same problem on theGillis' gallery, in that the slideshow button doesn't work:
http://www.thegillis.net/gallery/nova_purchase/

(Also, the search box doesn't work.)

Since the same problem exists when just loading the stand-alone version of gallery, I believe it's something to do with the file '/gallery/lib/url.php' that theGillis patched as gallery has no reason to use urls from Mambo components?

Anyone noticed this problem yet? or know of a solution?
I'll try to look into it myself, but if anyone has a solution or advice, it'd be much appreciated!