I haven't had this problem, but if you goto the Start screen and search for "pen and touch" under settings, there should be a way to reset the Pen settings. I'd try re-calibrating the pen, and seeing if those settings might affect something. It could certainly be a faulty pen, but I'd try messing with settings first.
I don't think the Pen has a battery or any kind of power, but then again I'm attaching my Pen to the AC magnet when it's not in use (and not plugged in). Maybe try that too?
Pen is not powered but is inductively activated. That is to say that it has an induction sensor in it and when it comes within proximity of the screen the coil is activated and the pen is detected. I suppose it is possible to have either the pen or the Surface be bad and not pick each other up.
I had the same problem once. I even tried to reboot. If you have a microSD card installed, take it out and it may come back. Mine did after I did that. I put the card back in and it hasn't done that again...
Lol. Guys (and Gals) the pen IS powered. You put two batteries (or should have) when you opened the surface. There are 4 batteries in it.
Didn't you read the instructions? Two batteries are in the pen area. Unscrew it. Then there are two batteries in the head. You have to unscrew the pen then once it is unscrewed, using a small watch screwdriver, unscrew the battery compartment in the head.
Try new batteries. The pair it.
To pair your pen, hold down the top button until the green light comes on. Then turn your sp3 Bluetooth on.