You're not doing anything wrong. I have an X3L (since 2009) and a JTV-59 (since last May). The initial thing you gotta do (and you did find this out) was to change your input away from just "Variax" as you were getting both the JTV models and the mag's at the same time. You can do this if you want to use a model for sound 1 and mags for sound 2 if you you do a dual patch. I never have done this. Make sure you have the X3L set with the latest firmware, as that is when you should see Variax Ch1 & Ch 2 available on the inputs display. Choose Ch1 -- on that one you can get the models or the mags by pushing the model button on the JTV. I believe on Ch 2, it is only the mags -- someone in the forums or Line 6 may want to comment on this.
The X3L patch control of the the models is possible, but not with the Gearbox interface. It works for the 1st generation Variaxes -- I used it with my Variax 300 all the time and was disappointed as you were when the JTV did not respond to those Gearbox settings. I assign the X3L to control the JTV model at the X3L pedal itself. I pull up the patch that I want to control the JTV with, and enter the input section with the INPUTS push pad just below the left PUSH TO SAVE rotary button left of the display. I then see the inputs screen on the display. I push the down on the curser button to the right of the display (the button has arrows Up/Down/Left/Right). Them I set the JTV to the model I want it to control, the push the PUSH TO SAVE button and make sure it's going to save it in the pedal patch I want it to. (I have had the patch it indicates be something totally different -- dunno why..) and then I test it to make sure it took.
I'm on the cusp of moving to the HD500 pedal, and this is one of the reasons, but also want to explore the (reportedly) better sounds of the unit and with the expanded contol capabilities of the JTV/HD500 combo, I'm getting ready to jump. I tried one last fall from Guitar Center, but it happened to be a flakey unit, and I ended up taking it back and backing away from it for a bit, as I had other concerns about some of the functionality in the X3L not incorporated in the HD500 design, but that's a story for another time...
Hope this helps. I have quite a few patches set up to switch my JTV models in my X3L, and it does work fine, just more tedious than it should be to set up. I would think L6 could fix the Gearbox software package in this respect, but probably won't as it is now a "legacy" device, so most upgrade efforts will go towards their current product lines. The X3L firmware was updated to recognize the JTV and make Ch1 & 2, but I think that might have been the most recent, and was in 2011.
Hey Line 6 guys -- I just took a look at the software download area and saw the latest X3L firmware version on there is 2.01.0, released 6/10/10 and it doesn't address the Variax Ch1 Ch 2 issue. The X3Pro latest firmware is version 2.10.00, dated 8/10/11 that does address the Ch 1 Ch2 issue for JTV's -- I know my X3L has the choice between Ch 1 & 2 for the JTV. Either this firmware works in both the X3Pro and the X3L, or somehow the X3L version got pulled off the list of available firmwares for the unit. I'm thinking th OP does not have this firmware in his X3L. Help him if you can, please!!
Thanks David. Subsequent to posting the original question, I found the document mentioning the problem with gearbox and the work-around. I noted, however, that the document was a year old, and so I had hoped that perhaps that had given Line 6 ample time to fix the bug--like most conscientious software developers. I personally find it maddening when hardware companies assume that all their users will immediately dump all their old equipment the moment they come out with something new. Then, when they don't, they punish their customers by not so much as fixing even simple bugs in the accompanying software.
From both a human standpoint and a business one, it poisons your customer goodwill. Perhaps in the short run it will move some more units of the new gear, but in the long-run, it will erode your customer loyalty, setting you up for abandonment once your competitors demonstrate that they offer just as good a gear and they provide better customer service.
Also, as you noted, the latest firmware updates only to 2.01 and it doesn't handle the issue mentioned with the ch 1 and ch 2. There is a manual listing for the variax on the pod itself, however, and though I haven't fiddled with it extensively, it does seem to force the variax model (though not the mags). Just a major pain to set-up, as opposed to the more elegant solution that fixing the gearbox bug would provide.
Have you made sure to install/update your POD X3 Live to v2.01 and checked all of the input options?
The POD X3 Live v2.01 flash memory update does indeed add the Variax Ch1 and Ch2 options, it just was not added to the release notes of that download. Selecting those options will eliminate the issue you describe using alt tunings.