Well here's a coincidence. BikesnobNYC wrote today about a new bike he just received from the Milwaukee Bicycle Company, including this:

"The bike was packed exceptionally well and there wasn't a scratch on it. It was also assembled exceptionally well before it was packed, so I didn't have to do anything except fasten a few bolts. Nevertheless, being a dunce, while installing the handlebars I managed to get confused by the shifter cables until I realized that they'd apparently been set up to cross under the downtube. (Unless I was even more confused than I thought. Either way, they cross under the downtube now, and they work, so I'm calling it good.)"

Since crossing the cables is evidently not something he commonly does on his many bikes, I conclude that I'm not crazy for wondering WTF with my bike.

At any rate, one of my friends did some internet searching and found that Sheldon Brown discusses crossing cables as a way to solve a problem which apparently I and BikesnobNYC have had all our lives without knowing it:

"Most bicycles with handlebar-mounted shifters run the rear cable on the right, the front on the left. This causes some awkwardness in routing the length of housing from the shift lever to the frame stops. Due to the need to allow these housings to be long enough to permit the bars to be turned all the way back and forth, the housings often wind up making a reverse bend--for instance, the rear will go from the shifter, which is on the right, swing forward and cross over past the centerline of the bicycle, then back over to the right side of the top tube, before heading down the down tube. These extra bends increase friction, and the fairly forcible contact between the housing and the side of the top tube can damage the finish.

A neat solution to this is to run the cables "criss-cross" style: The rear runs from the lever, (on the right) around the top tube, and to the cable stop on the left side of the downtube! The front cable crosses over similarly from the left side of the handlebar to the right side of the down tube.

The bare cables then cross one another under the middle of the downtube, making an "X". The cables may touch where they cross, but they will do so very lightly, since they are both straight...the tiny bit of friction at this crossing is more than offset by the reduction in friction in the smoother-flowing cable housings.

This technique does not work with over-the-bottom-bracket cable routing, but is doable with most newer bikes that have under-the-bottom-bracket cable routing and cable stops mounted toward the bottom side of the down tube."

(from http://sheldonbrown.com/cables.html)

It's still not clear to me why they suddenly felt the need to make this change on my bike, since as I said I've never had any problems before with the cables on this or any other bike. All I know is that the shifting was massively, hugely messed up immediately after they did it.

I will ask them about it the next time I have my bike at the shop, though I have no idea when that will be.

Thanks!