What version of After Effects were you trying to use?
Iv'e tried CC 2015, 2014, and CS6. All of them had the same problem.
I have experienced the same problem described here, and have not found a solution.
Surface pro 3
After Effects CC 2015 (and previous)
Everything seems to work properly, except for the way After Effects interacts with the surface pen.
It seems to register the first click with the pen, but not when the pen lifts. So, the cursor is stuck in a "held down" state. Once in this state, no more input from the pen registers. Only once mouse input is made does the cursor respond. With the "held down" state continuing until a click is input by the mouse.
After Effects functions correctly with input from a Wacom tablet connected to the Surface, however, with no trace of the buggy pen.
After Effects seems to be the only software that behaves this way. Photoshop behaves normally, Première Pro recognizes the Surface pen correctly. Flash CC gave me problems as well, but in a different way, related to the screen scaling, and not the pen input.
Hello ) I have installed all the latest version drivers and application but I have the same problem!
This problem exactly on the Adobe side, any other graphic software works great.
Sometimes it enrages me. I bought Surface Pro 4 (i7) specially for work in After Effects, Illustrator and Animate (Flash). None of these programs do not work correctly with new pen (n-trig).
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I HAVE THE SOLUTION! (I hope)
After Effects has always worked fine on my Surface Pro 4 until today... I hadn't used it for a couple of weeks so tried to work out what I'd changed in that time.
Answer is in Control Panel>Pen and Touch>Pen Options>Press and hold for Right Click
I'd disabled this, if you go into settings and re-enable this, it seems to fix the pen dragging in After Effects - phew
Hope this works for you