I've seen the process at some restauarants (though I don't know that it's the same at all restaurants), and what I've seen is that they have to key in the amount of tip, not the total amount. So if they make a typo (say, they didn't notice the .01 because they're not use to FTer-type rounding ), it goes in as what they typed for the tip, not what they typed for total (which looked rounded to you, but they weren't looking at the total, just the tip).

I've seen a circumstance where the total ended up .01 higher than I expected. When I reviewed my receipt, I realized I'd done the rounding math wrong, and indeed, if they had keyed in the right tip, it would have endup the .01 higher than it did.

Of more concern: I've had a couple cases where the restaurant failed to key in the tip at all. I'm surprised this doesn't happen more: I see so many restaurants where they're sloppy about putting away the receipts you sign, leaving them out on the counter where they're candidates for getting lost (the other day the next customer put her handbag on top of my receipt, I scooped up and grabbed it and handed it to the cashier, as without the tip I wouldn't have made $15!).