Its a texture issue, i recall back in my initial omnifactory days coming across this, researching and finding out that the GTCE owner didnt consider it his fault and wont fix it.
Avoidance is relatively simple albeit not always effective. Dont use anything other than GTCE tools on GTCE machines/blocks (including the chests etc.). classic examples include using dolly's etc. on chests, slapping a machine with pickaxe by mistake etc.
And yes the only know fix is to restart client, a few reload rendering etc. but it ultimately doesnt work.
This will affect any pack with GTCE with it. As such i'll tweak the tag/title.