Put it back to the stock tune. If the limp mode persists then you have something mechanical going on. If the issue magical goes away, then its the tune. If your tuner won't help you solve it, then go with someone else.
Tuner has me in contact with Sct, they are saying this is a very common issue and it comes from not having the tire size set correctly. I am not able to edit the tire size though, so they are reaching out with a support tech admin tomorrow to see if we can finally get this corrected.