Just got a hunch and found out some more info.
Latest Genome2D is compiled (incorrectly) with g2d_nativeContext.enableErrorChecking = true which means Stage3D will throw error even in places where it would otherwise ignore them. This is resulting in the sample 0 bind error. It can be easily reproduced by having GTexture with nativeTexture somehow disposed or null. However if I switch the enableErrorChecking to false it will no longer throw the error but just draw nothing instead, which is what older version of Genome2D was doing since there was no change to the actual draw methods for some time.
I will update the sources and SWC to disable the error checking, you can still enable it through getNativeContext if needed obviously.
However this doesn't answer the issue of having null/disposed textures there on your side, there doesn't seem to be error with texture switching either.