Hi all, im not sure if this will help but i was having major problems for days with mechjeb in both 0.20 and 0.21. After many many hours i found the culprit myself. Now it may not be exactly the same problem but could be a lead in the right direction. I used to have the control part to attach to ship but no menu tabs ever appeared. This is a copy of my post from a different thread that worked for me.
Ok, problem solved. Here is what i did. After days of messing around with this thing i finally found the culprit. COMODO Anti Virus blocks certain applications if it does not recognise its certificates. I tried telling it that KSP can go do what it wants with no restrictions but still didnt work so i just uninstalled COMODO, Uninstalled KSP 0.20 and reinstalled KSP 0.21 with mechjeb 2.0.9 in the gamedata folder. I then gave it a test and all works perfectly. I then installed B9 parts and NovaPunch2 and tested again succesfully.