I got it!  This morning I reflashed the guitar (yesterday I had reflashed my Pod xt live), saving the models already loaded yesterday.  I saved them because they were showing the alt tuning set up when I loaded them in the editor but the sound changes were not being applied to the guitar.

On the guitar I selected the Custom I position on the knob.  Then went to the editor.  The first model was in the edit window with the alt tuning reflected at the bottom of the edit window.  I pressed Enable.  I made sure to wait for the change to be loaded and for the yellow exclamation mark to appear above beside the first model button.  Then I selected the button near the top of the Edit window for the second model and repeated the Enable step for each model in the Custom 1 group.  That enabled the alt tuning for the Custom 1 models.  When I had changed all five models in the Custom I group I went to the tone locker and hit the sync button at the bottom.  All five models were saved to the guitar in about 15 seconds.  I sync'ed them one group at a time (e.g., Custom 1, T-Model, etc.) because I had had problems yesterday with some attempted updating timing out before all the changes were made.

I did the same with each of the other model groups, syncing one at a time to the guitar.

What a relief.  I have been working on Workbench and connection problems for three days.  One of the main reasons I bought the Variax was the alt tuning function, since all 550 pieces of music I play are written down a full step and it just makes everything easier.

If anyone else is having similar problems I would be happy to try to help.  Thanks, Scott