My guess is that the water level in your hydroton grow bed does not get as high as the level in your gravel grow bed. Search around on youtube, but I have seen a few videos where larger aquaponic operations intentionally raise the water level during the time they are trying to germinate the seeds. Essentially, we know that seeds need to stay moist to finish germinating. If the seed dries out, in most cases, the seed will stop germinating. You want to keep the seed moist.

You also mentioned it was winter. It takes a lot longer for seeds to germinate outside of their optimal temperature range, which in most cases is not colder temps; therefore, it could easily be the temperature as well.

For instance, lettuce has a 99% germination rate in 2 days at 77 degrees Fahrenheit; however, at 32 degrees Fahrenheit (freezing) lettuce has a 98% germination rate in 49 days. Weird right? You still have a high germination rate, but it takes forever. And in a grow bed, if it takes a while the seed can possibly get washed away or deeper into the medium in such a way that if it does germinate it doesn't have enough energy to grow into the light.

Your pH could also be the problem. If the pH is too far off it can denature the seeds. Seeds also have their own mechanism to detect the right conditions to germinate; so, maybe the pH didn't kill the seed, but perhaps it won't allow it to trigger germination.

I am sure there are a ton of other reasons, but I believe these are the most common.

I hope that helps!

REFERENCES:
http://tomclothier.hort.net/page11.html