Yes you can sit in the JAM EXAM as long as you have completed your Bachelor's degree by the time of admission.there is no problem if you have active backlog at the time of giving exam they just evaluate candidates on the basis of their marks in IIT JAM.you just need to submit your provisional documents at the time of admission and request them you will submit the marksheet after it gets declared as soon as possible.ALSO,You should have a valid Bachelor's degree in the relevant subject area by the time of admission to the M.Sc. program.