I would wonder if there's a pressure point or barrel contact change between the two configurations. I had a 700 that showed the same once, but it was the plastic Rem stock with the bumps in the barrel channel. Once I switched to a better, bedded stock the variance went away. The CDL stock is more stiff than the plastic one, but there might still be some difference.

Also possible that your two 3-shot groups are a statistical anomaly and if you had shot all of your rounds at the same target they would have just been a part of the larger group.

Last edited by joelkdouglas; 09/22/16. Reason: typo