I have a problem with the Ender IO Textures not showing the right ones when I use the Dense Conduits, they revert back to the regular me conduit texture which makes it confusing, I have tracked it down to foam fix, is there a option I can toggle to fix this? Thanks!

FoamFix has a lot of options! I'd be surprised it does anything to textures in this way, but I'd recommend fiddling with flags pertaining to textures and/or models.

I have managed to reproduce issues with Ender IO ME conduit texturing with just Ender IO + EnderCore + AE2 installed (no FoamFix), but I can't really formulate a clear enough bug report at this time. Could you double-check?