A couple of issues I've noticed - when I set a heading and turn on the auto pilot I note that the heading the plan will fly is off by a few degrees vs. what I have programmed.  Usually 2 - sometimes more.  Also, when I set the course for an ILS landing about 10 miles out the course will change automatically two degrees.  So for example, if the runway course is 189 - I program and at some point the software changes the course to 191....I'm confused so any help would be much appreciated.

For the ILS - looks like magnetic variation slowly changing over all those years: FSX = 2006; NGX = a couple of years later (= NGX navdata a couple of years "younger")

 

For the heading - heading, corrected by wind, results in a certain track over ground. So this track will most likely vary from your selected heading.

A couple of issues I've noticed - when I set a heading and turn on the auto pilot I note that the heading the plan will fly is off by a few degrees vs. what I have programmed.  Usually 2 - sometimes more.  Also, when I set the course for an ILS landing about 10 miles out the course will change automatically two degrees.  So for example, if the runway course is 189 - I program and at some point the software changes the course to 191....I'm confused so any help would be much appreciated.

Regarding your ILS course issue : in addition to what Oliver mentioned already, check out the paragraph on the SET FSX LOC CRS option on page 72 of the NGX Introduction document.  From what you describe, it looks like this option is active in your setup and the above paragraph in the document explains it.