Has anyone made an online payment that actually was posted and paid, but never cleared the bank?

I would imagine that the most likely explanation is that your bank posted it to someone else's account. They will eventually discover this and correct it. So, no, I would not add the balance back to your account just yet. After about 18 months, you can probably figure it won't ever be fixed...but not just yet.

Do not "just add the amt back into your checking acount register". If it goes through later, it might bring your real balance below $0 and cause your checks to bounce.

Their is only one explanation I can see. Did you have enough in your account to make the payment, or make recent deposits in your account that would give you enough to make the payment, If you did you usually have to wait until the next day for it to go though. When I make a payment online, it deducts the amount right away, and shows it as a pending transaction for a day or two, they usually receive my payment in a day.

Something like that happened to me a few years ago, but I never figured out the source. For nearly a year, my account balance was $140 higher than what my register was showing. Then, one day it was correct.