Have you kept them both in the exact same conditions? Same tank, tankmates, food, etc? I'm asking because we had purchased a golden dojo loach about 8 months or so ago (but at the same time as a co-worker bought her GDL). Anyway, we recently rehabbed the golden dojo she bought because apparantly it was being nipped by pea puffers. The fins were almost all gone, it was thin from being fed flakes (our dojos are fed frozen bloodworms or brine shrimp), and completely stressed out from being around those puffers and away from any other loaches.
When we first brought hers home, it was amazing to see how different the two were in size. Ours was at least twice as big as hers was. But after at least a month so far of good food, no stress (we have a strict community tank), and lots of loach cuddling (we also have 3 other dojo loaches), "Fish Stick"/"Nublet" (we call it both) has become a delightfully happy and not so little loach.
Just wondering if the conditions could have something to do with it? Just throwing it out there... Thanks.