What is a “capstone track” in a Master’s program?
Many software engineering programs offer the option of a "capstone" software project instead of a thesis to complete the degree.  This is typically a project that stretches over a full semester, or year, or even longer.  In my department, these projects are designed in cooperation with local industry, so there are real "customers". The  intention is that the project will force the student to synthesize all the skills and knowledge acquired in other classes in the program, and will give them something closer to real-world experience that a typical class project.  

As for "how is this different from a Master of Engineering", I have no idea.  Everybody gives their degrees different names; there is no standard. (My department offers a capstone project only for undergrads; the degree is a Bachelor of Science whether you do the project or not.)