Basically, what I refer to is this: one transformer will often be louder or softer than another, pulling the stereo image off center. In addition, when I've played low bass tones through them, one channel will sound different than the other - for example, the bass may be less solid and will sound more as a buzzy, second harmonic than a fundamental tone (in this case, 30Hz or 40Hz). I first noticed this with the Specos that originally came with the S.E.X. amp - I couldn't figure out why one channel always seemed a little louder than the other and the stereo image pulled a bit to that side.
Perhaps this really does have to do with variations in the laminations from sample to sample. These are $3 transformers, after all! I can't measure inductance, so it looks like I'll stick with the listening test to match pairs.