Sounds either over-gassed or under gassed.

Try loading one round and seeing if it always locks back.

And what do you mean by standard spring?  Rifle or Carbine?

You have to FIRE it with one round loaded, pulling it manually tells us nothing.

This test tells us if the bolt if cycling fully.  Doing it on one round at a time means you can easily do it a dozen times.

By this I mean only one round in the Magazine

First thing I would do is try a heavier buffer.  I would go straight to an H3.

The scratches are likely the teeth on the barrel extension scratching the cartridge as it is fed into the chamber. I doubt it is significant.  

You should easily be able to order an H3 buffer online.

Catch in front of the bolt face holding it back with the empty mag still in the well, or the bolt catch only on the bottom of the carrier instead.

If in front of thee bolt face when the bolt locks back, then the problem is not an action stroking problem, but either mag not recovering fast enough to get the top round back up tight against the feed lips (dirty or binding mag follower in the body  here), the mag not retained high enough in the action ( could be you are holding the mag as a hold point, and canting the back of the mag downwards to allow the bolt to run over the top of the mag, or even the mag catch not correctly installed with the threaded tip of the catch flush with the face of the release button), of could be that at some point from not cleaning and lubing the rifle correctly, the action is fouling up to cause a short stroke, then enough lube making it way to the fouled action to relieve the problem instead.


So lets get this out the way,
What solvents are you using to clean and lube the rig?  Same with pulling the mags down to clean them as well?
Also are you using a chamber brush with CLP to clean the chamber during cleanings?

What is a normal amount of rounds that you firing through the rig as one time, and are you re-lubing the rig as a certain point within these amounts of rounds?