I'm in the same boat as you. One of my recommenders wrote me a 3-sentence letter, ending it with "I am unable to evaluate her in an intellectual capacity." I work for him in a lab, and while I do a lot of analysis for the graduate students there, I haven't approached him with my own research ideas, which he took to mean I'm not interested in his field. So he wrote the letter like I'm an employee.
One of my other letters is super strong, though, and actually in the field I'm applying for (developmental psych...he's in auditory perception), so i'm REAALLY hoping that overshadows the crap letter.