I have a similar issue around some shortcuts that I cannot trigger. Examples are Cmd/Option/Control-A, Cmd/Option/Control-T.
Here are my troubleshooting steps:
1. Uninstalled BetterTouchTool (I did have some of these mapped through that app).
2. Uninstalled and reinstalled Alfred.
3. Restarted my Mac multiple times.
4. Looked through the Keyboard preferences to see if anything conflicted.
5. Rebuild macOS Metadata (in Advanced)
6. Clear Application Cache (in Advanced)
It appears that I'm able to set other combinations of CMD/OPTION/CONTROL, but not A, C, L, M, S or T. Anyway to figure out what keyboard shortcuts are in use in the system? Anyway to reset all of them?