Generally, sales of aircraft are subject to sales tax in Texas (just like cars and trucks). Normally the seller collects this tax as a part of the purchase/sale transaction. However, the purchaser is responsible for the tax unless they can show that the seller actually collected the tax and failed to pay it over. If the seller does not have a sales tax permit, then there would be no reason for the seller to collect the tax and the purchaser would need to make the appropriate arrangements. This is identical to the situation where you buy a vehicle from a private property - when you go to register the vehicle in your name, you are required to pay sales tax.
I would suggest that you provide proof of the purchase price to the comptroller and work at it from that angle to get the balance adjusted properly.