I know this is an old thread, but the only dialogue Munroe says talking to him in the control room that I ever got was the Starfleet brute line, and I always get 100% now on the first mission. I'll give you my usual playthrough:
Arriving at Espoir, ask Munroe to beam down. I don't think it matters what you say to Munroe and Breddel afterwards, but I usually say things to Munroe like Why are you doing this, how can a loyal federation scientist do a thing like this, and with Breddell is revenge the only thing you ever think about, and even with your goons you're too scared to face me.
Then you have to convince Sheme to let you out of the cell, you can do this by asking about his father, asking him to clear his father's name, then asking him how Breddel treats his friends. There's also other dialogure paths you can choose that work. After getting your equipment, go to the docking bay. Surrender and use Spock on the two controls and sabatoge them. Go outside the computer room, stun the guards. Inside, stun the guard. You have to "excel" at the chess game, choices: 1, 2, 1. Use both tricorders and then Spock on the computer to get the data.,
Go to the crew quarters, use the medkit on the sleeping crewman to drug him. Get the dummies. In the execuitve quarters, get the air filter. Go to the transporter, quickly use the air filter on the floor. Use the training dummies on the transport pads and beam to security. Talk to the head guard and choose choice 3. Use the science tricorder on him. Use Spock on the right console in the back of the room, then the chair controls and the one in front of the chair.
Go to Central Control, talk to Munroe for the brute line. Use the medkit on the technician with the allergies in the corner. Have Spock use the two controls on the side and the console in the front. Go to Special Projects, quickly use the kill phaser on the beast. Have Spock use the console. Leave the room and use your communicator, you'll get a message about the Alexander being on the way.
Use Kirk on the lock to Breddel's quarters. I pick dialogue choice 2 about morals. Stun Breddel. Take the dart board. Take his journal and tricorder the bookmark. Use Spock on the proto-weapon controls. And that should do it.