Maybe look into adding support for this mod as well:
http://minecraft.curseforge.com/mc-mods/231659-aquatweaks

I love aquatweaks but, even without that, something could be done, no? Mariculture and BoP have somehow avoided the issue with blocky coral - and they're also open source :)

I've noticed the tropicraft coral looks okay underneath regular water, so it must be something specifically to do with the tropics water.

This fix will be in v6.0.5 :)

For those wondering, it was an issue with how Forge's BlockFluidBase rendered block sides. I used vanilla's instead, worked like a charm.