With "CyclopsCore-1.9.4-0.9.0" and "EverlastingAbilities-1.9.4-1.2.4" only
Java Version: 1.8.0_111
MinecraftForge v12.18.3.2221

Regeneration 1 and 2 are dont work at all. Only regeneration wave animation and not a single HP regeneration for a 30 minutes. With this 2 levels of regeneration you can die from hunger.

Nothing seems to be wrong here. These are just vanilla's regen mechanics, which consume the hunger value.

Why every else ability in 1st and 2nd level work normal, but Regeneration is wasted. If you cant fix this, then skip first 2 levels of regeneration and start from Regeneration 3.

This is vanilla behaviour, if you're not satisfied with that, please report it to Mojang.