(Hey, Peter…long time no speak.)
I’ve also got this same problem running El Capitan 10.11.6, Cintiq 24HD Control Panel and Driver 6.3.16-12, and KM 7.2.
I have a macro, triggered by Control+s then injects a forum signature line (which is about 160 characters of text, no control or modifier keys).
The effect is that, when I run it, the keyboard (from any application programs point of view) goes into upper case. However, when I use the OS X Keyboard Viewer I can see that that the keys are shown in lower case, and the shift key is not stuck down. So it’s something between the OS view of the keystroke and applications’ view of the keystroke that is folding the keystroke to uppercase. I have also observed instances where it appeared that the Command key was “stuck down” as a keystroke modifier.
I have tried killing off the KM Engine process – that does NOT solve the problem – it merely prevents me from forgetting what I’m doing and accidentally causing the problem. The only workaround I have found is to restart the Mac.
For the moment, I have disabled that one particular macro, but I’m concerned that other macro triggers that use Keystroke Modifiers, will also trigger the problem, so, sadly, I’ve had to stop using KM all together.
I’ve not looked at other threads on this forum, so I’m not sure if there is a known workaround.
@Peter: Please let me know if there’s any diagnostic mode for KM or any log files etc. that I can retrieve and send you.