I own a restaurant and have observed a number of oddities with our credit card billings that have been explained to me as follows:

A guest check is generated on the core Point-of-Service software. When you give the server a credit card, the charge processing is handed off to a separate module of the software (some places do not buy this module). There may be bugs in the handoff process -- I have caught this after all the books for the day are closed, and the sales report still shows the rounded number for a transaction, while the card processing report shows an unrounded number for the same transaction.

POS systems can be programmed to round a guest check to the nearest nickel -- commonly, systems will round only tabs created by bartenders. This feature is supposed to save bartenders time when they make change. The actual bill that gets onto our books may still be calculated to the penny -- not the nickel -- depending on how meals/sales tax works in that state. This, then, may also affect the credit card transaction.

Still, I can't see why the actual charge slip, once generated/printed for you, would be processed for a different amount.

It is possible for a server to key in a different amount for a tip than what you enter. Usually a mistake, usually small money -- they have many, many more reasons to get the bill right than to try and mess with your bill.

Our most common discrepency comes from bad customer math. Makes servers nervous, because they're never sure what to do. example:

Subtotal $90.48
Tip (filled in by guest) $19.52
Total (filled in by guest) $100.00

So, the guest is long gone, and now the server is entering the tip into the system -- what does he do?