That's a reasonable response by your dealer if they are not familiar with the lender. There are many "certified check" scams going on right and it is far too easy to be scammed. And the "replica" checks being created by these scammers are IMPOSSIBLE to tell from the real deal by looking at it.
If they are unfamiliar with the lender, I can understand wanting to wait for the check to be cleared by the bank and the funds deposited.
My wife and I just got our dealers license in NH and we use and recommend
http://www.capitaloneautofinance.com a lot which I believe is the same type of service. There is one number (the same one each time) that I can call to verify the authenticity of check so I am comfortable letting a car go once I have verified the check with CapitalOne. Not sure if e-loan has this same service?
I would also hold the vehicle if it was a lender I had not done business with before. Having said that, it does see odd that a large dealer would have never used eloan before. But I don't think it is out of line to request time for the check to clear. Lot's of scammers out there these days it seems.
H3wannabe