I had a high dollar purchase recently shortly before the billing cycle closed and I did not want that balance to hit my statement, as the statement balance is reported to credit reporting agencies. That balance would have shown high utilization, which is a ding. I always pay FNBO electronically, using their website (I haven't written a check in years). The high dollar purchase was showing as pending but not posted and I tried to pay it. The website wouldn't accept the payment because it exceeded my outstanding balance at that moment. The attempt did not trigger any other action, though.
I spoke to customer service and they explained the website does not accept payments over the posted balance and to just wait until it posted. It posted the next day, which was the closing date, and I paid it. The large amount never appeared as an outstanding balance on my statement, which was my objective.
My experience with FNBO, which included disputing a mis-charge from a restaurant (vastly inflated tip), and relatively high dollar foreign transactions (VIA ticket purchases), is their customer service is outstanding. Much better than BoA, whose agents seemed to stick very tightly to their scripts. FNBO agents all seem to be "Midwest nice" and seem not to be or are very lightly scripted. They all have seemed to have a genuine desire to help.
I have no idea why they do not want to accept "advance" payment, but it is clear they do not. Perhaps it fits into a known suspicious activity pattern.
Once the AGR points are posted into your AGR account at statement close, they're yours. The bank cannot claw them back.
I doubt Amtrak will be changing affinity card partners soon. The switch from BoA to FNBO was just a couple years ago. I was initially suspicious of FNBO (which I had never heard of) but I like them better now than I did BoA.
Finally, most security holds, suspensions, etc are done algorithmically at all banks. No human is involved in the initial examination of patterns and initial security action. You are not going to get away from that by changing banks. I am a bit surprised an agent wasn't able to lift it, or transfer you to the security/fraud department, which has more latitude to act, though. Perhaps the pattern it fits is a very serious one and they locked that action down against human intervention for some reason.