The rules for Ender Lilies are actually extremely complicated, as it turns out. See this FTB Wiki page for a comprehensive description of how they work, at least in version 1.0.3c.
- If you have reliable access to enough Ender Core blocks, then always grow Ender-Lily crops on that. Otherwise, if you have access to End Stone, definitely grow on that.
- Only half of the growth stages can advance to the next stage at any given point in time, and they're staggered so you won't be able to grow a crop twice in a row (except if you happens to try at the boundary between sliding windows, which is always at a sunrise when growing on anything but Ender Core).
- Using a Watering Can on the crop for a few seconds should be enough to force growth if it's possible. Otherwise, the randomness of block updates could possibly cause you to miss growth during a time when it's possible for the crop to grow.
In other words, this crop forces you to wait a minimum amount of in-game time after planting before you can harvest it. For a crop planted on End Stone in the Overworld on a world that's hitting 20 ticks every second, the absolute best-case scenario outside of using Ender Core (which is very expensive) is that you plant it just before sunrise (50% of the time) and use the Watering Can, then it grows immediately, then sunrise happens and you use the Watering Can again and it grows again, leaving only 5 more growth stages to go through; sleep immediately when possible and use the Watering Can right after sunrise; do this until you can harvest it. All of this will take slightly more than 50 minutes ("slightly more" = it takes a few seconds to go to sleep each time).
If you have the time, read the FTB Wiki page for a more comprehensive explanation about what's going on.