It seems that clipboard/pasteboard history manager doesn't react to clipboard changes caused by other apps. For example Keyboard Maestro. So even if clipboard content was changed by other app, pasteboard history manager doesn't notce this. I think that when activated, pasteboard history manager should check if clipboard content was changed and then update used content.
BTT checks the clipboard content on certain events like cmd+c but also every 1.4 seconds.
You can test this e.g. using this terminal command which will put "this is a test" into the clipboard:
echo "this is a test" | pbcopy. BTT should pick that up.
BTT doesn't check more often for performance reasons (there is no way to be notified about clipboard changes), but maybe I can add an option to make it check more often for special use cases.
The problem is that when using Keyboard Maestro it doesn't work. I have macro changing underscores to dashes. After few seconds pasting clipboard shows modified value, but clipboard manager in BTT shows old one and using "paste as plain text" pastes old one too.
Maybe KM somehow changes the pasteboard without increasing the change count :-/
Not sure whether this will be fixable, but I'll have a look.