Did you try the qt.conf trick?
I guess you need to enable Windows Ink again and then do this:
Find the file “qt.conf” (probably here C:\Program Files\Animation Paper\qt.conf). Delete it or rename it (to save it). Then launch Animation Paper again.
This will force Animation Paper to use Windows Ink.
I’m not sure it will work – but definitely worth a try! Please let me know how it goes.