Duemion

I'm having a bit of a problem I don't understand. One of my rockets is built out of a base of my heavy lifter, which I loaded in and built the lander part on top of the lifter. On the launch pad, I'm able to activate the avionics in whatever mode I want to, however when I get to my 3rd stage(Decoupling of lifter from lander) all the options to activate an avionics mode become disabled and are greyed out. I thought it was because the root of this ship is a fuel tank, but I tested with other similar setups and can sometimes only activate 2 modes, or 1, or none. What I'm afraid of is that if I make a lifter, an orbiter, and a lander and i have to make the root part the lander then I can only have this mod active on the lander when it is seperated(Can't activate avionics on orbiter while lander is detached from it) Any thoughts?