I had the same issue and stumbled across this thread.
If anyone happens across this with the same issue, my problem was I had my task set to periodic. For some reason, single scan doesn't work with periodic tasks and I had to convert mine to continuous. I did not test with event tasks, but I doubt it would work. This is on Logix Designer v32.11 with Logix Emulate v32.00.
I placed my emulated PLC in program mode (it doesn't matter from Designer or Emulate), right click the PLC from Emulate, press Single Scan. Then put the PLC in run mode (again, does not matter, but I find it easier from Emulate). One scan will execute. You will get a weird pop-up (you may have to hunt for the popup if you placed the controller in run mode from Designer) asking "RUN Continuously? NO Single Scans Again". Press "No" and another single scan will run again. Press "Yes" and the PLC will return to normal behavior (i.e. scanning continuously). The only way I was able to run just a single scan and not return the PLC back to normal was to ignore the popup (not pressing either button) and return the PLC back to program mode from Designer.
Good luck all and as always, thanks Rockwell for fantastic documentation.