I have this same problem, using Cintiq Companion Hybrid.
I guess it's a low-priority problem but it exists and I wish a solution could be found at some point. Working with a pen switching from Photoshop and Spine pretty much sucks because of this and I often end up clicking things in Spine many times before it actually selects. And using Spine with mouse is awkward...
I have a faint feeling that this problem didn't exist a year ago. Either it's because I changed from Intuos to Cintiq or something else : O!