The issue is the read-write process the MetroCard uses. When you see "Swipe again at this turnstile" the amount of money has been deducted from your card but the write process didn't finish to the card with the time and turnstile number. The only difference with a booth is the way the card reader is a dip like a bus instead of swipe so the read-write is more secure and may work better. Also, turnstiles only update the station computer and station computer only updates the mainframe every 6 minutes (that's where you get the 18 minutes for multiple use) when everything is working correctly and the booth doesn't have the "Computer Down" on the dry marker board.
Most station agents after a single attempt will just hand you the form to mail in the card http://web.mta.info/metrocard/pdfs/form.pdf
I go with the debit card for my Transit Check and eat the dollar if I want to replace a card that isn't expiring.