Jordan,
I had the same problem..or should I say, I still have that problem. A man in Chicago, at a tournament, made a comment to me once. He said, "Boy, that girl plays good, but she's never going to get anywhere with that hitch in her stroke." I overheard the comment and immediately started noticing the hitch in my stroke. For months it bothered me, then I decided that it has probably always been there and to forget about it. After all, what does the guy know. The moral to the story: It's all mental. Once you noticed the hitch, now you are thinking about it everytime that long shot comes up. Because of that you are more aware of what is happening and you are almost looking for it to be there. Sometimes a change in your stroke comes up when you haven't played in a while, you change equipment, or you have stuff on your mind. All things that make you more aware of flaws.
Try practicing without thinking about it. Forget that the thought of a hitch in your stroke ever came up. Or, you can say to yourself "I have to put a smooth stroke on this ball" and become totally focused on what you are doing. They are two very different extremes, but either one may work.
Hope it helps a little.
Sarah