If you have a good clarinet repair tech in your area take it to him/her for a check-over. The tech should be able to determine why you're having a tuning problem. There are many variables when it comes to the clarinet.
Two questions that come to mind are if you pull out the barrel, to bring your clarinet in tune, how far are you pulling it out (if you can measure the gap in MM it will be helpful) and after you've done that how is the intonation across the clarinet's range?
I agree with Steve about us needing to know more specific details about your set up (kind of clarinet, it's age, barrel length, mouthpiece, your level of experience on the clarinet, etc) will be helpful. Otherwise, we're kinda shooting in the dark.