Interesting to re-read this old thread. I subsequently had the same thing happen to me as gfunkdave a couple of years ago, for exactly the same reason, but I did not recall this thread at the time. I called, did not have to wait on hold long, and got a competent and straightforward agent who knew exactly what the problem was, and even had "comebacks" for my complaints - "Why didn't you contact me when the card was declined?" "You opted out of email communications" (To be fair, I think I just didn't opt in, and don't even know if that was an option when I first signed up for this). "How can I avoid this in the future?" "Just put a backup payment method in your account online".
Of course a couple of months ago, my card was suspended again - my Transit Check card balance fell after purchasing an Amtrak ticket and a 10-trip LIRR pass for the summer season, and coincidentally I had cancelled the credit card I put in for backup.
So I knew how to fix it (I got the email notification as well!), but it was definitely annoying having to wait 24-48 hours for the card to re-activate.
And yes - agree that the agents in the booths can't do diddly squat with these cards (even when the message at the turnstyle is "see agent" when the card is deactivated).