Do you downshift a lot from a high gear into third gear? Like shifting from sixth to third? Maybe you have worn out the third gear syncro.
First I would have a BMW dealer look at it. Take a tech for a test drive and SHOW him the problem. Hopefully they will replace your trans. IF they do... you might inquire about paying to replace the clutch while they are at it. The trans will be off and you will only have to pay for the parts and maybe an hour or so labor.
IF the dealer refuses to replace the trans... I would try another dealer. IF that fails... try checking the trans fluid. Your problem could also be a worn shifter or shift linkage or even a bad(collapsed) motor mount effecting the shift link.