Does your craft have a signal processor? Normally it should be in the probe core. If there is none RT seems to be disabled for the craft. I had that problem with a part from sound rockets, but it was fixed in the mean time if I remember correctly.
The problem is that some wing parts mass goes into the negative when you reduce the size with tweakscale. You can check with the middle mouse button. You can counter that to some degree with that sturdiness slider far adds.
I seem to have similar issues. I'm using mechjeb2 to get every last bit out of it. I climb to 27km at a speed of 1650 m/s that seems to be the maximum I can get out of it using the air breathing mode. Then I set the pitch to 10 degrees and switch to rocket mode. Mechjeb shows that I have enough oxidizer for 1564 dV in Vacuum. I burn at full throttle until I reach an ap of 100km. At that point I have 767 dV left. Unfortunately the drag is still strong enough to rapidly decrease my speed so I have to burn continuously to keep my ap. I settled with an ap of 85km which left me with about 300 dV which was enough to circularize and a burn that brings me back in the atmosphere. I had better results with a pitch of 45 degrees when I switch to rocket. That left me with about 350 dV after the circularize @90km. What am I doing wrong? Please Help