I have recently experienced the same issue with my JTV59 (non-US). I am in a bit of a pique about it.
Purchased the JTV59 end of March, worked great, a defintie asset fore my gigging, but needed to add in open E tuning for slide work, so wanted to use the Workbench, which requires ver 2.0 of the FW. Turns out this was a mistake, should have just done it on the axe in the old FW. Anyway, two days ago decided to do the alternate tuning creation. Battery was almost fully charged, should not be an issue. Running 64-bit Win7 home edition on a dual-processor Intel platform. USB connected directly to the PC.
After some monkeying around with the software (pun intended) to get all the software ducks in a row, I got the flash updated, sort of. I received an error message box similar to the one below, but it differed in that it said the MIDI drivers were already in use and please correct. Or something to that effect. Uh oh. Unplugged the guitar cord to shut it off and disconnected the USB cable to the PC, then reconnected and powered up the guitar, ran the Monkey, which reported flash 2.0 successfully installed. Hm. Then opened the Workbench, it recognized the guitar, ok great. Created the open E tuning, assigned it to Reso G (not one I am likely to use), uploaded it (successfully, according to the Workbench) and shut it all down. I did not have my guitar plugged into an amp, I assumed it was all straightforward. Bad assumption.
Plugged it in last night to woodshed, went into model mode, and... no models or tunings. None. Just the same flat tone, much lower level then the mags. The LED selectror LED lights up as normal, and when I turn to ResoG on the Alt Tuning now the LED turns deep blue, but no models or tunings. At that point, just put it away, I wanted to woodshed my chops, not chase down firmware bugs.
So there it sits. When I get a chance, I wll try to reflash (with the guitar connected to an amp this time!) and try to get it to work, but... this is ridiculous. It should not be such a pain to do this, seems the much vaunted Line 6 technology is still a bit hinky and neds some fixes. When I bought my HD300 a few years ago, I tried to update the FW but it was so trouble-filled I gave up, it is still at ver 1.0! I will say the JTV59 models sound and play much better then the old models, they feel like real guitars, and in modelling mode the axe responds almost identically to mag pups,. And the mag pups are pretty good (just have to back them away from the strings to get them to open up). But the software/firmware issues are just plain silly. I am an EE by profession and deal with all kind of SW tools and rarely see anything that is as flaky as this. Well, maybe Windows. But come on, guys. I know it's just a $1000 guitar (!?), please fix this instabilty, if my company sold stuff this flaky we would be in deep trouble. Please fix!