Trying to get permissions on a certain content type to not conflict with Domain Access

I am using Domain Access to make multiple sites housed under sites.example.com. Domain Access shares users throughout (I'm using LDAP) and also shares databases... So my content is technically shared from john.site.example.com and sue.site.example.com. However, Domain Access has a section that allows content from other sites to be hidden to avoid confusion.

Once I activated another module called Content Access (because I need the users on one of these - share.site.example.com - to only be able to see content on login), my Domain Access hidden content all reappeared on all of the websites, regardless of which website had made the content.

Do you have any thoughts regarding this? Is there some shared code that conflicts between the two? Or is there another way for me to provide rules for a certain content type without conflicting with Domain Access?

thanks!