+1 on it likely being a mistake.
"Tune-up" can mean a lot of things in a lot of shops, but an annual service likely means replacing the cables and housings, and if they did that, then it's also likely that they pulled out all the old cables and housings, didn't pay attention to the backwards routing, and then installed the new ones the "normal" way without even realizing they'd made a change.
I think if it were me I'd have mentioned it when I brought the bike in, to make sure they were aware of it.
That said - I replaced my levers way back in I think February, and because the LBS offered me a great price including installation, I went ahead and let them do it. Should've done it myself, because they didn't put the levers back where they were. 
And they did such a pretty job of taping the ergo bars, whereas I'm such a klutz about it, that I haven't wanted to move the levers back, so I've been riding for the last 2700 miles with levers in an uncomfortable position.
Speed comes from what you put behind you. - Judi Ketteler