This is a bug that still exists today! Your fenix3 likely sync over wifi your activity skipping garmin connect which is where the intensity minutes are calculated and added to your profile.... Skipping the garmin connect means no new intensity minutes calculated for you.
It is not a bug, it is a feature. Intensity minutes are awarded for minutes spent in elevated HR zones, so you need a device with a HR monitor. You won't get any intensity minutes for kilometers logged on your Edge as long as there is no information abot your hear rate.
Of course, that's correct, but you still need the HR. Without the HR, there are no intensity minutes anyway. And if you have an HRM belt, you can link it to your watch, even if you do not wear the watch on your wrist, hence you can have the intensity minutes recorded with it.
I'm not sure that having HR is a pre-requisite. Before I got my FR945 this December, I had a Fenix 3 (not the HR model) and I distinctly have the memory of being "granted" intensity minutes even on days when I did not do any activities, nor wear the HRM belt. I just walked or moved around.
I have also validated it now by looking back in my daily summary, and for days where I wore my Fenix 3, did not do any activities I have still received intensity minutes. So I do think that you can gain intensity minutes - given that the device support it of course - even without recording HR.
And when googling a bit more selectively, I managed to find this - you gain it either with your HR or your step frequency.
https://support.garmin.com/en-US/?faq=pNU9nnDzzGAHmEavp9rpY8