Control inputs stop working!

[Hyperlynx]

My craft stop responding to control inputs all of a sudden. I press on the controls, I see the gauges change, and the vessel does not maneuver.

Piloted aircraft I have previously designed and flown will refuse to take off when they ignore the pitch up control, and probes I've launched into the upper atmosphere will refuse to answer the RemoteTech autopilot instruction to orient to prograde AND refuse manual controls.

The issue is intermittent. The probe I mentioned responded to the RemoteTech controls to get up to around 40-50km, the navball switched from surface to orbital, and then it ignored all inputs. I checked, and there was still plenty of electric charge and I still had RemoteTech signal back to KSC.

I have recently deleted and reinstalled all my mods using CKAN to cure another bug.

Mods installed:

I suspect the problem might be Ferram Aerospace. It seemed to be the cause of my previous problem, which was the screen going blank with the UI present and the velocity pegged at NaN. I tried to get it working again by reinstalling everything, and now I get this bug...

Also, when I start up, I get an "Incomatible Mods Detected" message, flagging "KSPAPIExtensions". I have updated all my mods using CKAN, so I don't know what this is on about...

- - - Updated - - -

Actually, probe goes out of control when I stage to the second-to-last stage. Again, I still have RemoteTech link and resources, so it's not pilot error

[Speadge]

try to check the navigation computer from remoteTech.

It happens that you lock your direction there and cant change it manually anymore (even if "local controlled")

[Hyperlynx]

The thing is, it stops responding to RemoteTech commands as well. I switch to "orient to orbital prograde" and it just spins. I cancel commands and try to control it directly, and it still doesn't respond...