There's nothing temperamental about the R3 and TuneECU starting or not. Load, key off, key on, start, works every time if you used the right base tune. I've done it probably about 500 times now between my two Triumphs.
I'd suggest verify that you used the right base tune! Sounds like you loaded a pre-2014.5 tune into a post-2014.5 bike or vice versa.
You can't mix old to new or new to old, and just because it says "Roadster" tune, doesn't mean it will work in all roadsters. It's stupid, it's frustrating, but its not terrible once you get it sorted out.