The problem is that there was some MS Word formatting in the notes that doesn't get deleted when you clear them out.

If you cut and paste job notes from MS Word that have fonts or margins set, they will affect the size settings of the note box. Moreover, if you then delete the notes that you have pasted, it STILL leaves MS Word code in the field, and it will push down the job, leaving a big empty space where the notes should be. If you DO paste in things from Word, and need to remove them because the formatting looks off, then select one of the templated job notes and then clear the box. That will ensure the MS Word formatting is gone.