This issue applies to any dependancies of uploaded assemblies.
 
Raised by: John Lambert - http://forums.microsoft.com/MSDN/showpost.aspx?postid=1542164&siteid=1
"This isn't a good idea in general: ...assemblies can depend on other assemblies and so it's better to use serialization to decrease the coupling."
 
Potential solutions:
 
Upload a Zip file in specific format.