Please note that the MP2 sounds library should be added to the main SampleTank 3 Library. That way, ST3 (and ST4) can load its own instruments and the MP2 instruments.
I'll guess that when MP2 library was installed a different folder path was chosen. If so then you could end up with duplicate folders, maybe empty ones. The path chosen should be the same as used in the ST3 library install.
As this is primarily a user to user forum, someone-else may chime in. Meanwhile, the best thing to do is raise a Support Ticket, here:
http://www.ikmultimedia.com/contact-support/mi/for some one to one help (US (East Coast) Business hours, generally).