I'm still having this issue, and have been for I think six months or so. Siri hotkey is not set to the same as my Alfred hotkey.
It sometimes takes about a full second for the Alfred input window to show up, and I often find myself typing my Alfred query into whatever text field I was previously in. Sometimes I hit the Alfred hotkey again because it's not showing up, which causes it to close as soon as it does appear.
Any other reason it might be taking a second to open? I remember it used to be lightning quick.