Sorry for not providing an update on this. In case it could help anyone I wanted to follow up.
Basically, the bank had no idea what they were talking about. It turns out the chanote was fine, but they needed official copies of the actual chanote. I have no idea where they came up with the "chanote is not normal" stuff. They said they sent someone from the bank to the land office and they couldn't find the chanote, and they weren't going to give us the loan because of this. After months and months of trying to make this happen and all the effort we put into it, we were pretty heartbroken. We had basically given up hope, but a week or so later we had to go to the immigration office and since the land office was nearby we decided to stop by to see if we could get more information before we totally called it quits. The people there were super helpful. They got the boss of the land office to work with us. He said the people from the bank are idiots and they never even went there. He got someone to go look for the chanote and after a while they came back with this ancient looking chanote. It was well over 100 years old if I remember correctly and everything was fine with it. We made official copies, sent them to the bank, and got approved. The next time we were at the land office we were signing papers and handing over cash. Now we have a beautiful home on the land and all is well.
So, you shouldn't always take the bank's word on things. I'm sure they're right the majority of the time, but in our case it was just a whole lot of misinformation and incompetence.