Seems to be due to what they call "cross use", any HMD other than the Index with the Index controllers will have the wrong controllers detected. Seems they've set controllers to be selected based on HMD and not on what the actual controllers are detected as.Mine are detected properly and I have no issues, outside of the gun angle being really strange but might be intentional.
have to say, the dev suggestion of using the Vive wands with the Vive and the index with the index "for now" is a bit annoying.