I had exactly this problem today, for the first time (9000 km, June 13 build). When I manually overode it, as you say, it did the right thing. After 10 minutes I set it back to auto, and all was well again. I'm getting the first service on Monday, and the dealer told me there is a flash for the hvac which they'll apply, although they will have no idea what it fixes - probably the hot/cold issue which I don't have. I think you should report as it's a bit hard to claim normal operation. Given how rarely (once!) it has occurred for me, I doubt I'll see any change - unless it happens again of course!
2014 JGC Overland Cherry Red Off Road Adventure Package, ARB colour coded bar, 265/65/18 BFG's