It may be a genuine bug as you say, but I know I've been caught out on numerous occasions by the fact that, when you change views on the green, it sometimes automatically changes the meter scale (but only occasionally - it doesn't seem to be very predictable.) It's really easy not to spot it when it happens, and impossible to tell after you've played the stroke.
It seems to 'guess' the right scale on the simple basis of length from the club to the hole, so on an uphill putt it may switch because it assumes you want a shorter scale than you actually do - hence the ball rolling significantly short.
Just a suggestion and I may be wrong! But since I started double-checking the scale just before every shot, I've noticed it several times and have thus been able to correct the error before playing the stroke. So that maybe worth trying - but then again, it may be a completely different problem!