How should lentil roots grow in a microgravity system?
It sounds like your first issue is with seed germination. I am assuming you are doing a seed sterilization. You may want to try allowing them to imbibe water for about an hour after the sterilization process, and then wrapping them with aluminum foil and placing them in a fridge for a day or two. I've done this with Medicago, which is another legume. However, not sure if it works for your lentils. 

The root may also have trouble developing given the micro-nutrients in the media. I am curious what recipe for media you are using, as the amount of agar may also affect the ability for these roots to penetrate the media. I have had trouble germinating legume seeds when there were 100+ seeds in a plate as they inhibit each others growth. 

It's hard to give a clear answer, but try optimizing your seed sterilization protocol and media recipe and best of luck!