To me there's too much smoke for there not to be fire.
1. Zoom has a thirst for speed force. Jay needs the speed force.
2. Jay pops up on Earth-1 out of the blue with no powers.
3. Jay claims Zoom was created by Wells-2's machine. Jay got his powers from Wells-2's machine.
4. Zoom needs Barry to be faster. Jay trains Barry on how to be faster.
5. We know Caitlin has ran tests on Jay and finds no trace of the speed force.
6. We know Jay has a counterpart on Earth-1 named Hunter Zolomon.
7. Jay disappears for odd stretches of time on a world where he knows no one and as far we know he has no powers, no car, and no home.
So to put it all together...this is all sleight of hand. Jay and Hunter are in cahoots (or Hunter is controlling Jay). One has powers the other doesn't. Any tests ran on Jay were really ran on Hunter. Anytime Jay and Zoom are in the same place Hunter is pretending to be Jay.
I'm Zoom. Jay is my Earth 3 counter part. lol, I'm joking. If he was Zoom, then it would be just like season one over again. Just like Wells and the guy in yellow.