I've had this happen lately, too. In fact, as an experiment, I was playing a patch with Axe Edit closed, then opened it while continuing to play, and the tone changed. It's a different thing, i know. Probably to do more with what happens when Axe Edit launches than anything, but that along with other glitches like the OP describes has got me doing most of my actual tone tweaking on the Axe Fx itself. I just can't take the chance that the tone will not get saved like I'm hearing it. I'm sure it will get better as the product and company matures. It's definitely not a big deal; I'd much rather have the major effort going into improving the Axe itself (though frankly, it sounds so good in 6.02 that I'm not sure it can get much better).