I'm having the same problem with Looper and Logic Pro X. With sync set to "INT", looper works as expected, but with sync set to "USB", the 1/16 and 1/32 looper functions don't work. In controller mode, Roller works perfectly with INT or USB.
Is this a bug, or are my settings wrong somehow? Everything plays/records in sync with USB, so I think my settings are good (used the Logic Tutorial Arturia put out). It's just the Looper (a huge draw for me) that doesn't work.