I'm not sure where the term originated at that restaurant, but it probably had nothing to do with Canadians' behavior since it was in a small Texas town that only saw an actual Canadian every once in a blue moon. :)
It may not be meant to make any sense. I worked in retail (probably like most people, ever) and we seemed to have a variety of signal-type words that made no sense to customers...or management. Makes the job more fun.
I'm pretty sure the origin is in irony because if someone overheard you calling them "cheap" or a negative stereotype there would be a problem, but if you we overheard calling them "Canadian" it's a lot more benign. I've heard "Canadian" used when working in restaurants outside of Texas, so I think it's fairly common in the US.