When I troubleshoot BTT keyboard shortcut, I usually keep a disabled version with the same shortcut keys assigned. This has worked fine for more than a year, until recently, say in the past couple of months. Now, some versioned keyboard shortcut will lead to a beep but no action. It looks like the disabled (grayed out) keyboard shortcut is somehow called by BTT. If I delete the disabled keyboard shortcut, the remaining enabled one works as expected.
I cannot recall when this starts to happen, but I first noticed the problem during the winter break. It took me a while to figure out the root cause. Most disabled shortcuts are not producing interference, but some do and the interference is getting more often.
I am not sure if this bug is related to a recently resolved bug of Specific App Did Launch. There, multiple "did launch" actions interfere with each other. My BTT preset is about 1MB, the vast majority being keyboard shortcuts.