This behavior has been happening to me as well. It might be a system preferences/modifier key problem - when I use ⌘+L in firefox to place the cursor in the address bar, I often lose the first character or two of what I type next, if I type quickly.
This behavior is most noticeabled on Alfred, because I use it constantly, but it might not be an Alfred bug.
If anyone else figures out the problem, even if it's not with Alfred, might you add solution?