I'm going to have to blame this on quality control, but I've seen significant differences in bottles of different sizes at the same time that have aged for 6 months or more. These are specifically IPA/2xIPA that i brewed and then bottle conditioned in whatever I had on hand (22z vs. 12z vs. dogfish hellhound style (750ml?))
I can't guarantee that they were stored the same, or that something else didn't affect the perceived flavor. Given Revvy's comments I'm going to pin the culprits on 4 things - different rates of oxidation due to storage conditions (heating and cooling can cause air to transfer under a beer cap over time), poorly mixed bottling sugar causing uneven distribution, more yeast in some bottles vs others (first fill vs last fill), or different foods consumed while tasting the beers.
It *seems* like they are different, but without doing repeated triangle tests for beers under the same conditions, there's no way to prove that the bottle sizes make a difference. I've also never had this with my force-carbed beers, which leads me to believe even stronger that this is a QA problem in my bottling/storage process.