Can you elaborate? short term calculating as long term  or vice versa ??  

are you entering the sale and purchase dates backwards?

I have not had any issues with this.

Yes it's calculating all of mine as S (short term investment) even though they were bought 12 years before they were sold. Did you figure it out? Thanks.

Clarification - you are entering on 1099B Worksheet Quick Entry Table  - correct ?   What are you entering in 8949 Box  (where you select A,B,C,D,E, F) ?   is this possibly forcing it to Short Term?