you have to set each tone to either force the variax model... or not force the variax model....

i suspect that you are not forcing the model and the variax stays as selected.

stolen from vettaville:

Controlling Variax Settings in each POD X3 Live Patch

• In each patch (bank/channel memory) you have the option to have the POD X3 Live control the Variax or allow you to control your Variax. If you would like to manually control your Variax, you can.
  
  
• While in the INPUTS screen, select the lower half of the screen. You will see the word MODEL in the bottom left hand corner. If you don't want the POD X3 Live to control your Variax then rotate the left-most control knob under the screen until you see the words DON'T FORCE MODEL appear above the word MODEL. This means that the POD X3 Live will not force Variax model selection for this particular patch. You will have to manually control the Variax.
  
  
• If you continue to rotate the left-most knob, you will see that you can scroll through the Variax models. You will also see the word TONE appear next to the word MODEL. Use the left-most knob to select the Variax model that you would like to assign to the patch that you are editing. Use the knob under the word tone (second from the left) to adjust the default Variax tone knob setting that you would like to assign.
  
  Tip: To speed things up, if you are wanting to select a Variax model from the Variax User bank (U prefix) then just use the Variax controls to select the model and tone dial setting for the patch you are editing. If, however, you want to use one of the Factory bank (F prefix) models then you will need to scroll to the Factory bank models using the POD X3 Live.
  
  
• Once you have assigned the Variax model and tone knob setting for the patch you are editing, press the PRESS TO SAVE button once to go to the patch name editing screen or press it twice to save the setting without editing the patch name.
  
  Repeat this process to assign Variax models to your patches (bank/channel memories).