Craft switching causes engines on previous craft to still be controlled

[ghost]

I've encountered an issue where, after I undock 2 craft, increasing the throttle on one craft will cause the engine on the other one to also fire.
This seems to be limited to while the 2 craft are still within a certain range of each other. However, if I undock, move out of range, then move closer again, the second ship engine begins responding to throttle commands again.
I have some video footage of this occurring, if it's of any use.
I'm using KSP version 1.2.2 with the dll modified by Taniwha for that release.
I removed all other mods except this one and still had the issue. Removing this mod then fixed the issue, however this causes massive lag on my Saitek X56 joystick, so I have to continue using it.
The only way to get around this happening is to go to the Tracking Station and reselect the ship from there. If I 'quick' swap from ship to ship in the map view, the issue still happens.

[deram]

Also controls still go to craft after starting EVA. Though this could be considered a feature, but then it would be nice to be configurable.
(MacOS Sierra, KSP 1.4.1, Thrustmaster T.16000M)