Command Pod/Control Module Explodes at 66km

[RocketBlam]

I'm trying to launch a rescue mission. I do this by putting an unmanned capsule under a control module, so I can launch it unmanned.

In this case, every time I hit 66km, one or the other just explodes for no apparent reason. Whether I am under power or not, when it hits 66km, one of them explodes, usually the control module (the command pod only exploded once).

The only mod I have installed is MechJeb, and it explodes whether Ascent Guidance is running or not.

There is no apparent reason for this... I've even turned off all the SAS/torque wheels on the vessel.

Strangely enough, after the control module explodes, I still have full control of the vessel, despite the fact that the command pod is unmanned.

I think they might have overheated on ascent, somehow, although not sure why they would wait until 66m to overheat. I launched again with MechJeb Ascent Guidance, and noticed that MJ's "Limit to Terminal Velocity" trigger was going off at really low velocities for the altitude. I was at 21km, only going 400 m/s and it was slowing the engines down. Have the aerodynamics changed that much?

Edited May 1, 2015 by RocketBlam

[RocketBlam]

ETA: I think it is an overheating problem. I relaunched after redesigning the craft, moving the command module inside the storage bay. Also, when launching, I didn't accelerate as fast as before. It made it into orbit.

I suspect it had overheated, but if this is the case, then it should have stopped heating up well before hitting 66km.