In short, your waiter said what he said because it is the "in" thing to do for young workers (mostly part-time) at inexpensive restaurants, fast food places, convenience stores, etc.
This speech style is called 「マニュアル[敬語]{けいご}」, 「コンビニ[言葉]{ことば}」、「ファミレス言葉」, etc. and it has been very common the last 20 years or so. (マニュアル = "manual", ファミレス = "family restaurant")
マニュアル敬語 is basically a set of honorific expressions that are not really "correct" by the traditional (or school) standards. Many young kids seeking employment are not good at honorific speech to begin with but the employers mentioned above have no time to teach it as it is not really their job. So, instead of letting them speak freely to their customers with their terrible honorific speech, they ended up creating "their own" simplified honorific phrases instead and the result is devastating IMHO. It sounds like a whole new language for people who are old enough to have kids working at those places. It has been criticized in the media quite heavily but it does not look like it is going out soon.
Using the past tense to confirm orders is one of those "rules". I cringe at it and so do many others but we hear it on a daily basis.
「Aランチのほうでよろしかったでしょうか。」
This sentence has not only one but two problems in it.
1) Use of past tense in よろしかった.
2) Use of の[方]{ほう}. That is completely unnecessary.
"Traditionally" the waiter would confirm your order by saying:
「Aランチでよろしいでしょうか。」
and that is exactly what a waiter would say at a more expensive restaurant.
No one knows how many more decades this speech will last but I personally feel embarrassed that this was pointed out by a Japanese-learner.
There is even an article on this on English Wiki, which means that it is one huge phenomenon.
http://en.wikipedia.org/wiki/Manual_keigo