Jared,I there any way that you could create a small sample that reproduces your behavior? I have been trying to reproduce on this side and I am just not able to make this happen. The sample doesn't have to be robust, just reproduce the problem. I am sure that it would consist of a website and a BO class library and then a page with a combo that is trying to populate from a BO in the class library. Though I think I know the components, I just can't get it in a reproducable state.
I have seen things like this before when there have been issues with the StrataFrame database not being updated, but it fails accross the board (Win and Web) and from what you have mentioned, it works on other sites. I have also seen this when there was a reference issue and the class library could not be properly reflected.
I might do two things if you cannot re-create this. First, download the 1.6.5 update so that we know that you are running the latest build of SF. Second, if that doesn't resolve the issue (which I don't think it will), you would be well served to convert your website to a web application project....NET plays much nicer with a web application than a site...ESPECIALLY in regards to references.
One final thought, if you are using source control delete your local instance entirely, then redownload from source control and to a rebuild. I have also see issues where old assemblies get stuck in the bin or Obj folders that could cause this type of behavior as well.