I am going to take an educated guess at an answer... I need to submit this as an "answer" because I want to include some screenshots to clarify my response.

It sounds like you might be using the Export wizard to create the JAR file (screenshot below) instead of generating your JAR file actually via Maven which is accomplished by Run as... Maven install (second screenshot). If so, I'm pretty sure there is a fundamental difference in what happens via each method.

Can you confirm how you are generating the JAR via comment before I augment this answer?