It definitely seems you are doing homework. Congrats. Most homebuyers don't spend much if any time doing research, even of the public records.
While it is true that short sales typically sell for less than a house in a conventional sale (recent statistics indicate at least 20%), there are some market participants that seek to obscure the facts. Be careful.
No matter what you do, I would highly suggest you retain a competent Realtor who is experienced with short sales. If you are inclined to go it alone, consider retaining a certified appraiser experienced in short sales with knowledge of Saint Charles to determine the market value before proceeding. At least you'll what you are dealing with because the appraiser will spend the requisite amount of time and undertaker a greater level of detail than what you've done and perform analysis to arrive at what the appropriate short sale discount and market price.
PahRoo Appraisal & Consultancy
As far as the PIN # goes, you need to have a Real Estate lawyer and your lender check on this. The county assessor's office should be able to give the accurate PIN # and it can be straightened out with the proper procedures in place. A lawyer is the best one to help in this one.
The purchase price in 1999 isn't relevant. It is likely the owner refinanced at least once or more since then, likely taking out more money from the equity in the home (during the bubble many homeowners treated their homes like ATM machines so they could buy cars, TV's, etc...). Additionally, after commission and seller closing costs, the seller's lender is going to net a lot less than the purchase price, so even if the sale price was for the loan amount (and again, it probably isn't), a short sale might still be necessary to get them out from under their loan.
I doubt the listing agent is doing a scam. They might have obtained bad info from the seller to get a wrong pin# or taxes. Your lender, attorney, and agent for the transaction will protect you from getting in too deep with a scam anyways. Earnest money has very strict guidelines as well. But you do want to make sure you have a qualified real estate agent representing you to make sure you have legal protections. As a buyer, remember that the seller will generally originate the cooperating commission for your agent, AND this is a short sale so the lender will usually pay it, therefore, you have nothing to lose and everything to gain by using an agent.
I would be happy to help you with this transaction. I have sold homes in St. Charles before. Give me a call. At the very least, I can help you verify some of the (bad?) information you have gotten from the seller's side. Again, it won't cost you anything to talk to me.
Anthony Cavalea IV