I always change macOS Siri search to Command - Space. I was using Alfred long before Siri and wasn't going to break muscle memory. I verified that is the case on the problem system.
Interesting, the lag happens on every key combo I try EXCEPT Option - shift and I tried about 15 different combos. Option-shift is too cumbersome to use. Switching Control-Command between Spotlight and Alfred - Command Space has no lag, but I have years of muscle memory where it works (and it still works on my laptop). Grrr. I would rather deal with the lag than change muscle memory.
Seems like a system problem rather than Alfred's. I'll email you the diagnostics file regardless, but feel free to disregard.