I have already talked about this in my #90 Post that mechjeb 2.0 will not work at all, there is no sidebar, no window, it doesn't write to the plugindata folder, nothing.

We're aware of issue #90, but Mechjeb works fine for us, and we can't solve a problem we can't see. Perhaps you could try MJ2 on a different computer — if that works, you could investigate what's different between the two computers. (Have you checked file permissions, for instance?) In the meantime, I'm going to close this as a duplicate of #90.