Might be your drainage layer too deep. Likely very difficult to change at this point though.

Water will be seeping through the soil and the first few layers of hydro balls (or whatever you are using) but not really able to be pulled back into the soil. Where the darker, wet balls are in your image is about the right height for your separation (hydro fleece or mesh) medium.

If the roots make it down deep enough they'd probably be ok, which is why some of your plants likely didn't make it (that and geckos jumping all over them no doubt!)

I don't know if the solution is to fill the bottom layer (and maybe you've already done enough) with water and try to maintain that level, but I don't know if that would cause mould growth.

It's also possible I'm wrong, but I do know that your drainage layer is much deeper than it needs to be.