Hi,
My personal experiences are the same as Adman's, on both accounts.
Once, I was on an ORD-TPA trip which was delayed by 2.5 hours. I politely, with a smile, asked the gate agent if my (already cleared) upgrade could be comped due to the delay. She made me feel like a lunatic for even considering the thought. I did have a trip a couple of years ago at DFW which was late and they did comp me though I had to ask. I've never had an upgrade comped without asking so my guess would be that your case was an oversight ... or a particular agent who went that extra mile on thier own. By the way...my "on-time percentage" on AA lately has been about 50%, so there have been plenty of opportunities.
SAT constantly upgrades me (on the short SAT-DFW hops) whenever I volunteer my seat; whether or not they end up "buying" my seat back.
If there's one thing AA is consistant about, it's being inconsistant.