Yea - I am happy I found out about it now rather than at the airport. I have you and the forum to thank for that :)
Based on what a number of people said, I am not going to try to drive over the day of our flight - too stressful. But all this talk of driving through the Andes got me to wondering if I should cancel a day of wine tasting and do a tour in the Andes instead???

Roxanne I am really lost you bought a ticket to Santiado and then a ticket from Santiago to Bs Bs.>?
There is no point saying it now for this trip but for anyone reading a good buy is to buy the ticket from the US including Santiago Mendoza, this way it is almost free and no problem what so ever. Sometimes I buy Miami Santiago Mendoza Buenos Aires and from there Miami it is a good deal. Sorry about your problems.
To give you and idea of the fee, one day my Santiago Miami flight was delayed , or something happened that I had to stay a few hours in the Santiago airport and I would have had to pay the fee, so unfortunately I stayed at the airport. The airliner paid for lunch and I bought a book. Sad. ..

I had a similar problem with Lan last week. I bought r/t BA-Iguazu, and r/t BA-Mendoza because the two tickets were $550 and if you buy the ticket as one it was over $800. Anyway, when we checked in in Iguazu to go to BA and then Mendoza, I tried to check the bags to Mendoza and I was told, since it was not one ticket we could not check the bags to Mendoza. We had to retrieve the bags in BA and then check them, again in BA to Mendoza. The real stupid part was that we boarded the same plane we arrived on from Iguazu with the same flight crew, to fly to Mendoza. Go figure. But to answer the question 45 minutes will never work, and you cannot check your bags through unless you are ticketed all the way.

I haven't bought my ticket yet. I am looking at going from NYC to Mendoza (it stops in Santiago). I am going to buy one ticket straight through. There are 2 flights, one with a 45 minute layover (I was thinking of not checking bags??!!) and one with an almost 5 hour layover...

If you are thinking of not checking bags be sure to verify the carryon weight restrictions for international flights, they can be VERY restrictive.

Of course if you are doing a lot of shopping maybe it's only a problem on the way back!