Two Buddypress themes on a Multisite not playing well together, help?

I have a WPMU setup with two sites. Each theme is set up for buddypress and I want to share users/groups/forums/etc. between the sites. The main installation is meant to be a standard social network. The 2nd installation is using a buddypress theme designed to be used as a learning management system (LMS) and with course delivery modules. With both themes activated, links and a few others things go haywire.

The course module plugins that make the LMS side function are activating on both sites. When I create a course in site 2, it does not show up in site 1. Groups function fine between the two.

I realize I'm not doing a great job of explaining what I'm trying to accomplish here. Any ideas would be very much appreciated.