First of all, make sure that you have downloaded and installed the latest version of AT4.
Then, run the separate custom Shop program, log in, select the AmpliTube tab, then click [Gear] and select "Restore my gear". Check in Custom Shop that all the expected gear is listed. Then load the new gear in AT4 and check that all is OK.
If not, then 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).