They've always played it quite slow, since it's quite a slow song on the album. But, I've compared the live performance of Spark Arena to previous live performances in 2009 and yeah, they've always played it slightly slower than on the album, live performances at Munich, Saitama (Tokyo) and Pink Pop were comparatively quick/slow. I think during the 99 Revolutions Tour it was then played quicker again (see live at Reading or Rock Am Ring), but now it's slightly slower once more.
I also noticed that they played it marginally quicker on the second night in Auckland than on the first, but it's only a tiny difference.
I think the problem is, they've become a lot more consistent when it comes to tempo. This means, if they start out at a certain speed, they'll most likely remain at that. So, when Billie does this 1, 2, 1234 thing with the crowd, it gives him quite a slow starting tempo... Their playing on this tour has been a lot more precise and consistent than on the 99 Revolutions tour, where it was more sloppy and less consistent, therefore however more energetic...
Btw. coincidentally this is my favorite song too!