Can you give specific details. otherwise we would only be guessing.
-- Double-check that all the SOunds Library files have been installed
-- In the Custom Shop program, do a "Restore my purchases"
-- maybe some of the new Multis make use of synths in Syntronik 2 MAX?
I would think that Legacy Multis (from Syntronik (1)) would sound exactly the same. As they do for you, please raise a Support Ticket, with examples, for diagnosis.
For fans of the original version, all of the Syntronik and Syntronik Deluxe legacy presets are also included and sound identical in Syntronik 2.