Hello Les57,
I think you are close to the solution, even if it does not seem so. The fact that QuicKeys remains disabled tells me that "quick stop" does work for you. I also sometimes get transpositions after stopping QuicKeys, but only within a short period (10 seconds?) after I stopped it. From then on, there are definitely no more transpositions. If you do see further transpositions, could this be because you run another conflicting software (TextExpander etc.)?
If QuicKeys doesn't come back on after you say "quick go", it seems that for some reason the AppleScript is not being carried out correctly. You have several options to test that. First of all, you can of course change the commands from "quick stop" and "quick go" to whatever you like, perhaps phrases that are easier to recognize for Dictate. Second, you can install the versions that give you feedback using growl notifications. This is helpful to verify that the scripts were actually run correctly. To make this work, of course, you need to install "Growl," but this is not particularly difficult. You can find it at http://www.versiontracker.com/dyn/moreinfo/macosx/24638.
As a further test to see if "quick go" is working, I suggest you paste the code into AppleScript Editor and click the "Run" button. This test would eliminate any problem of Dictate recognizing the phrase that activates the script. To verify that both scripts are working correctly, you can use the utility "Activity Monitor," which resides in /Applications/Utilities/. In the middle of the main window (which you can bring up by CMD-1), there is a pop-up menu that will probably show "All Processes" when you start Activity Monitor. Change this to "Active Processes" to see only the active processes of your system. Click on "Process Name" to sort the processes by name. Find "QuicKeysUserEventHelper." Now, when you run "quick stop," this process should vanish(!) from the list because it is no longer active. Conversely, when you run "quick go," the process "QuicKeysUserEventHelper" should reappear. First see if running the script from AppleScript Editor does this correctly, then try to reproduce it using Dictate, perhaps with your own (better) choice of the command name. Back to the first issue -- getting transpositions even after halting QuicKeys -- another test would be to check if "QuicKeysUserEventHelper" is really inactive while those transpositions occur. I would be surprised if it was, but let's see.
Thank you very much -- on behalf of everyone else having this problem -- for contacting MacSpeech. I'm not too optimistic about a quick fix, either. As to who may provide a solution, it seems interesting that Dictate and QuicKeys cooperated nicely under Leopard (at least for me).