I was in a similar situation with one of my BoA accounts. I have been a customer of BoA for over 10 years and one of my accounts went into the red and was closed while I was out of the country. When I came back I paid the account and BoA said they could not re-open that account. I went to a credit union here in Atlanta and they refused to open my account because Chexsystems reflected that I still owed Boa Money even though I had paid. It took about Two months trying to get Bank of America to report tha the account was Paid to Check Systems. I tried to get BoA and Chexsystems to remove the entry in total but that was not possible. I took a printout of my report back to the credit union and they open an account for me. I think based on my experience you should be fine as long as the amount owed was paid. Credit unions give people chances that the big banks refuse to offer, and I believe most of them dont mind that one's has a record in chex systems as long as the account is paid and there is no money owed.
I've been in the red before and have never had my account closed.... That alone would make me never want to do business with BofA.
With Chase I was in the red almost 2k one time... but I had to get plane tickets for work. Chase was cool, I paid my OD fee, and brought the account back in the black like 4 days later.
I was in the red for a couple months - not just a few days. I understand why they'd close it. Weird part is that I was able to open an account with them again shortly thereafter. Honestly, they may not be all that great in some regards, but the truth is that they are everywhere and incredibly convenient since I travel a lot.
I must be crazy or unusual or something but I have had nothing but positive experiences with Bank of America and will continue to keep my checking account with them due to easy online bill pay and wide ATM network.
On one occasion back when I was in college my account was overdrawn but I was never hit with a fee. My xbox live yearly membership hit my account and I forgot about it. Luckily it was on a weekend, and my paycheck was direct deposited on Monday so I was able to bring my account positive before the charge cleared.
As long as my checking account remains free I will be a happy BoA customer. I'm definitely a fan.