I complement you on being an aware customer. Many persons would just take it and say nothing. Questioning like this may shake loose a slip up by a restaurant skimmer.

I suspect that in this situation, there is probably no cause for alarm, the restaurant point of sale system is not linked or "updated" or they changed merchant banks and that is the reason they are not linked together. It probably cost money to get them to work together.

It is more common to have your credit card "skimmed" in a restaurant by a device such as this

http://www.tyner.com/magnetic/msr500m.htm

The merchants of such devices imply that there are legitimate uses for these things, but I have not seen such and I routinely examine them containing customer's credit card numbers.

Also the trend in the UK and Europe and I hear Mexico is this type of parasitic device on an ATM

http://www.utexas.edu/admin/utpd/atm.html

Lastly, I have seen what I call a PS2 connector style hardware Key logger installed on some Point of Sale machines. Basically, they install them inline when no one is looking and come back to recover their loot(credit card numbers) at a later time.

I suspect we will see either
A change in the way credit cards are processed (i.e. moving away from the mag stripe)
Or like Mexico does today, they bring the portable point of sale machine to your table and you swipe your credit card. This was done due to the problem of skimming in that country.
RP