My first suspicion was the footwell module, but it sounds like you already replaced it.

Since all the symptoms are related to the climate control, the next area to check would be the climate control module. Can you check to see that all the connection to the climate control panel are secure? Unplug and reconnect to ensure proper contact - in case there are any intermittent connections.

Hi guys and gals sorry to be a pain but started the mini r56 again this morning and no heat from blowers. Yet I can leave it a few hours and it'll work fine. Im sure its electrical as sometimes the climate control panel works and sometimes not. The fusebox clicks its knackers off and the windows don't work. Yet few hours later i can de-mist windows with the de-mist button on rear windscreen and use windows and get hot air no issues and no fuse box clicking....then next time flashing lights on climate console and not responding and clicking fusebox....ps new frm module fitted 2 weeks ago but still same issue