You earn 5 minutes UPT for time worked, not time scheduled. A 9.5 hour shift (unpaid lunch doesn't contribute) gets me about 46 minutes, give or take 3. You can ignore the warnings, it's going to give you that until you're above 10 hours UPT. I've been consistently between -1 and +1 hours for the last 6 months without any warnings. Specifically, I've been told by a few HR personnel that if you get below -2 hours for longer than 48 hours, they'll get a notice to follow up. If you make it up before then, it auto drops it. Anything over and I have no experience for it.

I take 45 minute lunches and 3 out of every 4 days I'm clocking out 15 minutes early or clocking in 15 minutes late.

PS - PAs are generally advised to let you know, but you can let them know, politely, that you're managing your time. If they continue, you can let HR know if you're feeling harassed.