Shouldn't the carbonated bottles have a layer of yeast on the bottom? I would think that would be an easy thing to check.
Ok, well, to make a short story longer, there was some yeast left, but the yeast wasn't carbonating well. This actually happened last year, and we've since changed our yeast for a more robust yeast for bottling high alcohol beers. We've found that a random bottle will have great carbonation but the others are flat and sweet. They all tend to have yeast, but the ones with the fresh yeast (I'm guessing) seem to be the ones that are good.
I know it's too late for this time, but if you mark the level in the bottle with a sharpie, you can actually see when it is carbonated, because the level raises up an eighth inch or so.
Hmm, unfortunately it is too late, but that is an interesting observation.
The only thing we have noticed is that some of the less filled bottles (ie a bit more headspace) seem to have carbonated a bit more ... and are less sweet. We tried shaking them a bit and looking at the foam, but there really didn't seem to be any noticeable difference between them. May have to just chalk this up to experience.