the screenshot says it all ;-)

No not really. It doesn't say what version of EnderIO and RFTools you're using. In addition did you also report this to the EnderIO people as I have not seen this behaviour with other machines so far

Sorry, EnderIO-1.10.2-3.1.180, rftools 1.1x-5.92
i report it immediatly to the enderio people.

BTW, Not saying it is EnderIO's fault. But it helps to debug this to figure out what they are doing differently

Nothing special about those machines. Normal block model rendered in the cutout layer.

SleepyTrousers/EnderIO-1.5-1.12#4157

PS: With the level of detail available, I'm tempted to randomly guess+blame Optifine and be done with it.

it also happens with rftools powercells end endergenic generators. see in screenshot. indeed a lot of blocks are effected: stained glass, iron chestes, water, ...

Are you rendering in renderpass 0? That will only work for solid TESRs. Not that pass 1 is much better, in that case you'd render in front of all translucent blocks...