Hello,
How did you bind your native library, with FFI, alien or NativeBoost ? I guessed FFI but I'm not sure.
Did you try to run all the images on several VM (1 VM per image) ? If so, did it solve the problem ?
What version of the VM are you using ? (Evaluate Smalltalk vm version). Retry with the latest stable version of the VM and check if it does not solve the problem (latest stable here:
http://files.pharo.org/vm/pharo/, select your os then download stable).
I'm not sure about the overwriting problem, I'll ask other people on thursday (if they don't answer).