Breaks all template shortcodes

Hi,

I'm happy to see the new pro sites is up. However upon activation it simply breaks all my templates' shortcodes.

I used to have the supporter plugin. Since my site is still under development, I have opted to just delete the old files (within the mu-plugins directory) and upload the new ones in the wp-content/plugins directory. and then activated it.

Interesting thing is that it only does this to my main site. I have a subsite installed using the exact same theme and that one is working properly (shortcodes and all)

I also tried deactivating the theme and reactivating it, but I get the same issue.

Am I missing a step here?

UPDATE
Ok, so I tried some more tinkering. What I did was update the options on the Settings page of the Pro Sites Plugin. I did change a few values around but I am pretty sure just hitting save would do the trick. Maybe a developer can look into this and maybe patch this.

thanks

UPDATE 2
After creating a new user and site using the register from buddypress and selecting yes in prosites, when clicking on the dashboard for prosites,the user gets directed to the Prosites choose membership page. That page has all the shortcodes broken again.
The main site still works ok. The relative path for the problematic page would be /?bid=5