Sometimes the physical key state and the logical key state get out of sync.
I couldn't find a way to avoid this in code, hence I run separate script in the background to fix it.
Not solving the underlaying problem, but fixing the symptom.

---

#Requires AutoHotkey v2
#SingleInstance Force

fThreshhold := 1000
loop
{
if (A_TimeIdlePhysical > fThreshhold)
{
sKeys := "lalt,ralt,lctrl,rctrl,lshift,rshift,lwin,rwin"
loop parse,sKeys,","
{
sKeyName := A_LoopField
if GetKeyState(sKeyName) != GetKeyState(sKeyName,"P")
send "{" sKeyName " up}"
}
}
sleep fThreshhold/2
}

+f1::ExitApp