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I've had Citi CCs since early this year, pulling payments from a Chase checking account. I also had autopay set up, but generally paid statement balances manually before the autopay kicked in. A few times the autopay did kick in, so I'd definitely set it up correctly.
A few weeks ago, I added a Citi checking account for their $400 promo. When they moved me from a CC-only login to a "full Citi" login (which, in itself, was quite a headache), they lost all records of my from-Chase-checking autopay settings. Fortunately, I was just paying some bills manually before a bit of travel (just in case) when I saw Citi had no record of the autopay settings, or the Chase account from which to "pull".
Just a reminder that in 2016, autopay can still fail.
Citi's website has never been top of the line, for sure --- I'm surprised to hear they changed your website around when you upgraded from CC to CC and banking. I would think it would be the same, though I never banked with them.
Their website has always been kind of glitchy so the autopay fail doesn't suprise me much sadly.
I see Autopay as a backup not a primary. Like those automatic braking systems appearing on cars now. Sure, it will stop the car, but I would not want to count on it for day to day driving.
I do my payments way ahead of the due date. Autopay is for if I get hit by a truck and am in a coma for week sand cant pay.