Noticed a quirk in the latest version using the new "Unload Hidden Textured" feature. If I used a state to toggle on two layers using the same texture (Two animated sprite sheets used for eyes in my case) one would get replaced with a solid color box.
I was able to fix this issue by Saving the layer set, closing RahiTuber, relaunching RahiTuber, and then going to the problem layers and resetting their file paths and sprite sheet settings. So far it hasn't been back.