Agreed on the variables - same comp, different year, so yeah - different judges. These are some seasoned competition guys - one of whom won a gold at NHC. One says any time he feels he wants to get a true read on a beer, he bottle conditions the entry - he just suspects that an obviously clear bottom will be treated differently - just like a higher, over-filled neck, for example. It gets noticed and draws a comment, even if not overtly dinged; he just wants the presentation to be the best it can be and avoid some potential bias.
I see his point.
As to two entries - easily solved if two guys are involved in the brewing and one kegs and the other bottles their respective entries. There are still plenty of other variables, such as fermentation differences, etc...but you could close the gap on those to see if the bias exists...