Hi Cowboy - that's very strange, because the dialog you're seeing is normally only seen when you save a script as both an application and with "startup screen" checked in the save dialog (in Script Editor).
As far as I know there is no way around that startup dialog *if* you've saved a script with it enabled. I'm curious if there might be some configuration situation on your machine such that a different script is actually being run when you hit the shortcut vs. the menu selection.
Here's something to try: invoke the script with the keypress to get the dialog ("Run or Quit"). While this dialog is displayed, I am willing to bet that your script is being run as an application, and that an icon will appear for it in the Dock. Find that icon in the dock and Cmd-Click on it, which will reveal the script file in the Finder. Is this is in the same location as the one you are selecting from the menu, etc? Go back to the script and quit it. Now double-click the item that was revealed in the Finder. If it *doesn't* produce the same dialog, I'm very curious to have a look at it. Maybe you can send me that particular file so we can be assured that I have the file compiled in the same way, etc.
As for the speed question, I don't think anything has changed for the worse in 2.2.6, but there's always the possibility that I'm missing something. If you can identify a particular type of script that is slower, it might help. For instance, if you're always saving your scripts as applications, then the script launching time is largely an application-launch issue. The speed that FastScripts is able to add by caching the AppleScript code in memory is lost when the script is launched as its own application. I did make a change in 2.2.3 where I started treating AppleScript applications as true applications. Previous to that, I would extract the script code out of the application and run it natively from FastScripts. This could have made things faster, but it was at the expense of some desired benefits of running as an application.
For maximum speed I suggest saving all scripts as "compiled scripts," not as "application."