Jon - I have that trouble too. It seems like every fiddle or mandolin tune I start to learn these days has a "sticky" part in it that I really have to work on, while the rest of the tune falls in place fairly easily. And I can never predict where it's going to be. Sometimes the simplest sounding lick is the stumbling block.

This seems to happen more and more often as new tunes are learned -- I suspect the brain's memory banks start deleting duplicate phrases so as to be efficient.

I have learned to be patient and eventually the mind and the fingers agree (sometimes after months) to cooperate.

As suggested above, playing them over slowly seems to build the nerve paths that lets you go to autopilot. Sometimes humming the phrase over and over seems to help. This is like writing out the words longhand to a song you're trying to learn. The more you can involve the various senses the better.