After making some newsgroup postings and researching a bit. I found out some info that might be a contributing factor to our problems with assemblies getting referenced correctly.
In our assemblyinfo file we are auto incrementing the . From my reading, this attribute is actually meant to BREAK combatibility. What we need to be using is the This can be incremented w/o breaking compatibility and still help us figure out what DLL we are dealing with (which version).
This blog has an entry about it.