With the "You're kind of freaking me out," I would suggest that the 're was said too quickly for the person to catch.
On the other hand, "How you doing" (pronounced howYUdoo'n) has become a greeting, though usually spoken in jest. I feel like it came from some gangster film or commercial or something. Maybe in the local accent the 're in "how're" just got swallowed, so we picked it up with the verb at all.
Student or Learner