Can you take a look at the runtime logs (sorry, I'm not fluent with Docker) and see what happens at the CMD node ./nodebb activate nodebb-plugin-my-plugin; node ./nodebb build; node ./nodebb start -l step?
It sounds like maybe when ./nodebb start -l is run, NodeBB is doing another dependency install, which can happen if it detects some dependencies as out of date. That would effectively clobber your plugin that was copied into node_modules/
