Hi Marius,
This sounds an lot like the thread below (ignore the posts up until March 4th of 2010):
http://channel9.msdn.com/forums/TechOff/22266-Side-by-side-screwup/#Page=2
A recent Hotfix was released by MS, which could mean that your build-machine is trying to reference a DLL that won't be on your customer's machines. Maybe it's the same thing, maybe not. But, it sure sounds like it could be related.
-tom