Wild guess here... Crops up with me sometimes.
You may have a condition known as "Zombie Fingers". People with this condition have electronically 'dead' skin, such as musicians with callouses, on parts of their fingers. Rarely happens with thumbs. Charge buildups and dead zones are patchy and in close proximity, confusing the screen.
I am a musician, and can experience this when learning a new classical guitar piece, or after violin sessions.
Others who can suffer this to various degrees:
- People with cold hands
- Medical or food service workers who use the antiseptic hand cleaning stations often.
- Active swimmers (salt-chlorinated pools or ocean)
- People who craft with their hands
- People with pacemakers (can block capacitance in fingertips)
- Artisans or painters who must wash hands often, stripping away natural oils.
- People who get a wax or cream buildup on their hands, such as hairdressers, auto detailers, cleaning staff, or cooks.
By the way, a capacitive touch stylus, such as with the Surface Pro 3 (unlike your Surface Pro 2), carries a voltage potential all the way from your hand through the pen, concentrating it at the special nub. If your pen works properly, it is likely that your Surface device is fine.
Even a piece of sausage might work as a test.
@Runic12, go visit a shop which sells Microsoft Surface products, or find a friend with a SP2. Try one out. You will find out immediately if it is indeed you.