Did you speak with the eTolls people? I've had to call them before and they were unnervingly helpful - took about 2 minutes to bring up the full record of charges, corrected a very large mistake (similar to yours - I had a charge of about $90 appear on my card from them due to "unpaid" charges). There was no detailed questioning from them at all, and the credit appeared on my credit card statement a couple of days later. I've had 2 other similar calls with them to correct charges.
I was expecting the worst too.