All of the above mentioned items can cause an issue. BUT, you said you were using a CMMG Mk9 lower with a Colt upper. Just for fun, check to see if there is a drag mark on your BHO. (The spring loaded piece that pushes up and locks the bolt back when the mag is empty. CMMG did use a slightly different height on that part. I know I ran into a problem once when using a CMMG upper on a Rock River Lower and while researching I recall hearing about this. I do recall I did have one of my 9mm carbines that actually had a "witness mark" where the bolt was rubbing the BHO. I couple of file strokes to the BHO cured the problem and all was good.
One quick little check you can do regardless is to push out the lower pin while you are having the binding occur and slow raise up on the lower to see if the bolt gets freed up. If that happens you can then locate which part is causing the issue. Its super simple to push out the hammer pin and remove the hammer to eliminate that part.
Good luck with it.