I believe the hormone is a very likely explanation for the slowed growth.
20% biweekly isn't really the best plan for fast growth of fry. I understand the 'sensitivity' issue with the fry, but if you have been keeping up with water changes prior to their birth, then the tap water is pretty closely matched to their tank water... and so water changes should not actually be a shock to them in any way.
I'd suggest that 20% twice weekly would be more appropriate, but like I said, I haven't dealt with gudgeon fry in particular, but am speaking more about fry, in general.
Just for the sake of discussion, Ian Fuller (aka 'Coryman), an ichthyologist of particular renown on the corydoras species suggests that fry grow out tanks should have 50% water changes daily, if not twice daily. He suggests using water from the main tank, rather than tap water to be used... and that makes a lot of sense, given that it is probably closest to the water that they were hatched (or at least spawned) in, and where they will be going. This water will be free of the growth inhibiting hormone, free of chlorine, and the pH will have stabilized from any other gassing off processes that may need to take place.
http/www.planetcatfish.com/forum/viewtopic.php?t=8726
So, it might be worthwhile to do a couple tests on your main tank, versus the fry tank... and compare their values. If they are fairly close, you could probably use water from the main tanks and not worry as much about shock for the fry.