There is a rendering issue with Ender Utilities inventories and other mods.

Screenshot #1 (hotbar with a mix of items from Thaumcraft/Not Enough Wands)

The items render correctly (as they do in a the vanilla or baubles inventory).

Screenshot #2 (When you open a EU bag, you get this)

Thanks :)

Versions:
MC 1.8.9
Forge 1765
EU 0.5.0
NEW 1.2.9
TC 5.2.4

This is a known issue, and it has been fixed in my development version already. The fix will be in the next release, 0.5.1. Thanks for reporting though :)

Fixed in version 0.5.1.