I can replicate this with following on the new ß58:
Create a custom trigger and bind to a keystroke. I've only noticed this with CTRL-A, CTRL-C and CTRL-H, which are bound to AppleScripts on my machine.
Set the scope of the script to "enabled in selected applications" and enter one app. I set my triggers to be enabled in Mail only.
Pull up the Keyboard Viewer and press the key you bound in step 1. Your key combination should be highlighted. For me, if I bind a trigger to CTRL-C and press CTRL-C in the Keyboard Viewer, it does not highlight but every other CTRL- combination gets highlighted when pressed.
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I think this is the same thing I’m seeing when I attempt to disable a trigger in specific applications. For instance, I use ⌃⌥⌘V to bring up the clipboard history, but in TextMate, I prefer to use the built-in history (which uses the same shortcut).
Excluding TextMate does prevent Quicksilver from showing it’s clipboard history, but TextMate’s doesn’t come up either. My guess is that the scope settings for triggers prevent Quicksilver from preforming the action, where what it should be doing is preventing Quicksilver from capturing the keystroke at all. (Or as a work-around, maybe it could capture the keystroke, but then pass it through to the active application if the scope doesn’t apply.)
Thanks Viewer. I just tried that but no luck. If I add two identical triggers with the same keybinding, quit Quicksilver then relaunch, the trigger is still active in all applications. If I delete one trigger, the trigger is no longer active, not even in the target application.