Did all of your frames seem to vanish when you saved? Good thing you duplicated your animation, right? lol. Same thing happened to me the first time I messed around with Animation Shop :D But never fear, there is a way to fix it!
   Now, go to Save As again. Name it whatever you want again, and click on Save. This dialog box will pop up, as before:

   This time, click on Customize. Look at these pictures and make sure they match the ones in your animation shop's preferences.

   Make sure you set the colors up to 256, and click on optimized octre.

   Just uncheck all of these, you do not need to worry about them.