If dependent assemblies are in subfolders, I guess they are pointed by manifest with relative publickey token (that now you changed).
Try updating publickey token in manifest for dependent assemblies ... look here for more info:
Code:
http://msdn.microsoft.com/en-us/library/0ash1ksb.aspx
and here
Code:
http://msdn.microsoft.com/en-us/library/4191fzwb.aspx
Regards,
Tony