Yes, on firmware 2.0 there are issues (well documented by Martin and others ) as noted above. I guess it works on some guitars, but not all. Certainly not on my 89.
You can save yourself a ton of time and frustration here by just using the 1.9 software to create alternate tunings on the guitar (ie without workbench). This works fine, you just give up the 2.0 model guitars.
Here are caveats I've found as a beginner trying to make custom tunings under 1.9 that are not in the user manual:
1) Make sure the volume is turned up high when you make the tuning.
2) after you have 'saved' the tuning according to the manual, reboot the guitar, ie pull out the 1/4" amp cord, wait 10 seconds then plug it back in before you attempt to start using the guitar. This is kind of like rebooting a pc after you've installed new software, you shouldn't have to do it, but in the old days you had to.....
Hopefully the 2.0 issues will get fixed, but until then this works OK.