Some of my keyboard shortcuts no longer work!

In the main menu, check out the MIDI / Keyboard mappings by selecting Control > Edit Keyboard/MIDI Controls…

Verify that a keystroke is assigned to the commands you are interested in. If you notice that the keystroke is blank for your desired command, you can double-click the command and try to re-learn it.

If there are duplicate entries for any commands, then your command list has been modified accidentally by a recent change to Capo. If that's the case, then you need to quit Capo, and issue this command at the Terminal:

defaults delete com.supermegaultragroovy.capo CapoPlaybackCommands

Now re-launch Capo, and the commands should work as expected.