Have you got the very latest firmware on your X3L?
If so, then you will have 3 INPUT choices for Variax for each patch. The default is VARIAX which for a JTV will give you both mags and model sounds - so if you have an alternate tuning selected you will hear BOTH that AND the standard tuned strings through the MAGS which will sound awful. To ensure you only get the alternate tuning model sound, ensure that the INPUT selection for the patch is set to VARIAX CH1. If you have a dual tone patch, make sure INPUT 2 is set to SAME or the also VARIAX CH1.
If you just want to hear the standard strings through the mags only then you can pick VARIAX CH2.
Hope that fixes it for you.