I has a problem where one of my simple 2 letter aliases would yield Unknown Command. Sometimes 2 out of 3 times. I noticed that if I typed it more slowly it would work.
What I found out was that if Autocomplete is turned on and you don't give it the time to bring up the Aliased command. You will get the Unknown Command result.
I improved that by setting AutoCompleteDelay to 0.01 seconds. Now I can almost never hit enter before the command is autocompleted.
I think this kind of negates the idea of having a delay at all. But.....