Paid Under Protest?

My fiance and I just recieved the receipt yesterday for our 2003 Homeowner's Taxes (I can't think of exactly what it's called right now)

On the receipt, in big bold letters, it says:

PAID UNDER PROTEST


We didn't pay under protest... we just had the mortgage company take care of it the same way they have every other year. We know that the payment was made on time, so it wasn't that it was late.

He's going to call City Hall later today to find out what's going on, but... does anyone know what this means? What is Paid Under Protest? Is this going to reflect badly on our credit, mortgage, etc. if we aren't able to get it removed?