1. Worked fine for me just now. (Can't recall anyone else having a problem like this.) Have you tried it with a blank copy of the original template?
2. Are they pressing the numbers quickly enough one after the other? If yes, then it's a Sibelius issue. Are other shortcuts working/not working?
3. Your Playback Configuration may have become corrupted - known issue, not sure what may cause it though. Create a new one and see what happens. If continues, delete the "Playback Configurations" directory in the Sib User's folder, restart Sibelius, then rebuild the config(s). Open a copy of the original template, or load a TriggerTest file, then test away.
I don't believe the issues you've described here are due to any errors in the Template, otherwise many others would have similar experiences. Like I said before, it appears something has gone awry in Sibelius itself.
Have you sent me file(s) to look at yet?