Solution 1:

If a dictionary has it, that dictionary is just trying to be so comprehensive as to include any word ever. However, incapable is the proper and original form, and furthermore, everyone uses it. I have never seen uncapable in use.

http://ngrams.googlelabs.com/chart?content=uncapable%2Cincapable&year_start=1800&year_end=2000&corpus=0&smoothing=3

The rule of thumb to go by is: If you're choosing between variants of a word, pick the variant most widely used and understood. So when you have to choose, choose incapable.

Solution 2:

I came to this site because I ran across the word uncapable in the writings of Mother Theresa. She speaks of God talking to her about becoming a sister of the poor. "You are I know the most uncapable person, weak and sinful, but just because you are that I want to use you, For My Glory! Wilt thou refuse?" Unable, unsuited, unskilled, unfit, unqualified are all synonyms of incapable. But somehow this non-word, uncapable, has a sense of a void or emptiness waiting to be filled, rather than the feeling of incompetence that the word incapable gives.