I'm not sure if I'm missing something, but if the dr has an LLC, then the LLC would have a type II NPI for the group name and EIN, and an individual NPI for herself. The group NPI belongs in box 33A and the individual in 24J. When you say that if you put the individual NPI in 24J it automatically changes it in box 33A, how do you know that is happening if you are submitting electronically? Are you getting rejections? If so, are the rejections stating that the individual NPI is in box 33A? If so, you need to contact your electronic vendor or clearinghouse and see why the loop for box 33a is being populated by the NPI you are entering in 24J.
Since you actually are not filling in the form on the screen it must be in the way you have the information input into Medisoft. Start with your vendor. They should be able to clear up the problem.
Michele