[Por_sha911]

OK, let me get this straight. The gov't automatically overcharges you for your taxes and you then have to file paperwork (or pay someone else) every year to protest it down to the correct amount? Why wouldn't the protest carry over from year to year? Back in 2009 my county decided that they weren't collecting enough money and they raised everyone's property values by 10-20%. I was floored that in the middle of a housing bubble they wanted to raise my property value. Everyone said "you can't fight city hall"... I protested it and met with the appraisers with documented proof that values went down versus up. They adjusted my tax value down that year and it has stayed down at that level. Sorry, I got off the original question.
No, you don't owe them anything. They were notified (and admitted as much). You probably should have gotten something in writing to protect yourself. I suggest that you contact the company. Tell them you want to do what is fair and you will consider payment if they will send you a letter specifically stating that although they have it on record that you notified them however they went and did the protest anyway. Once you get the letter, consider it for 10 seconds and decide the fair thing is to not pay.