I had the same problem many years ago when I fitted one of John Bowketts long silencers to a Titan MC010. The rifle was fine without or standard or short length silencer. it turned out to be the bore relation.
Also when testing a couple of Steyr 10mtr match rifles from a test rig, indoors, I found if the barrel weight was moved forward by the permitted 50mm the groups would open up quite dramatically. I put this also down to bore relationship because the rifles were unaffected when I tested my 50mm sight extensions which fit into the barrel sleeve.