Any material added to the MaterialOverride.cfg becomes unusable in either the Part Builder or the Casting Basin. Material is still listed in Pattern tooltip.

Tested with latest versions, no other mods, and otherwise default configs.
Forge Log: http://tny.cz/f6575cf9

Okay, looks like that's reproducable. Thanks a lot, this'll make the issue solvable I guess.

Somebody give me a desk so I can headdesk thoroughly. Of course the equality check on instance breaks, if the material-override replaces all the materials >_>

Will probably wait for the next tinker update with this, but yeah. Fixed!