KSP x32 or x64 [0.24.2]
MechJeb2 [2.3.0]

take a rocket that flies normally (I encountered this last night with a super-heavy lifter - that was working flawlessly.

Mount something upside down to lift it to orbit (so that its crew capsule is upside down) and it veers out of control within 300m (altitude) of the pad. every time.

Initial testing was with a probe chassis [RC-001S, Probodobodyne HECS] as hub and then a crew capsule [MK1-2, MK1] mounted upside down above it. including directly to it. Further testing showed that it happened if the hub [MK1-2, MK2 Lander Can] was crewed and upside down. Still further testing found that sometimes if i have two crewed capsules (one as hub) then the

further testing finds that smart a.s.s. exhibits the same behaviors with an upside down [MK2 Lander Can] and anything other than kill rotation. (for example surface, 90:90:0). With a normally oriented can that command works great but with an upside down one - it veers into oblivion.

Here is a tree of my gamedata directory (Because it might be helpful) but i verified with a clean install + mechjeb :)

BoulderCo\CityLights
BoulderCo\Clouds
Chatterer
CommunityResourcePack\Karbonite
EnhancedNavBall
EnvironmentalVisualEnhancements
Firespitter
KerbalEngineer
Mechjeb2
NASAmission
NavyFish\Plugins\PluginData\DockingPortAlignment
OpenResourceSystem
Squad
TextureReplacer
TriggerTech\KerbalAlarmClock
UmbraSpaceIndustries\Karbonite

if you switch to IVA view inside the capsule it changes the control point. also when docking it can cause a problem as you have to control from a port and if you switch it can realy mess things up.

OOPS. I left part out. it should read:

Still further testing found that sometimes if i have two crewed capsules (one as hub) then as long as the upper one is upright it works normal, switch them and it dies in flame. with our without capsule torque turned off.

Also, kill rotation doesn't work very well at all. lol

Try this for me: Put two capsules together in such a way that it causes them to flip out at 300m. Confirm this is happening.

"Launch" this craft, but before liftoff right click the capsule that is oriented in the "correct" direction and select "control from here". Does the autopilot still have trouble?

This appears to fix the problem. if i have a probe case carrying the capsule into orbit and its upside down and i right-click on the probe casing it no longer crashes out of control. an unexpected feature (Mechjeb apparently really prefers crew capsules to control flight) but at least we know why it is happening :)