If you have the option of leaving it alone, then you probably should, however if you've already got to work on the messy part anyway, and if the code is messy to the point of being difficult to read, then you might be reducing the chance of introducing new bugs if the first thing you do is refactor the lot such that you don't cringe just looking at it.

I'm talking about cleaning up the code though, not the logic - refactor really isn't even the right word. Poor choices for variable names, misleading or just plain wrong comments, inconsistent use of whitespace, etc etc.

And even this you should only do if you really think it's necessary, since it will make it very difficult to use diff to suss out what your actual changes to the area were after you're done. Still, there is a time and a place for it.