I'm having the exact problems and I thought I was going nuts, only it's worse than this.
I contacted and finally sent the amp to Line 6 to have them test it. I got a call yesterday from the tech saying it works fine on his "Asus." I told him what I have (a custom PC with Win7 and plenty of everything you'd need to make a small program like the Utility work, as well as my HTC One M8 phone) and he said something about "flash" and that was that. Well, I got the amp back today and not a single thing has changed. The utility updates nothing even though it doesn't need to because I borrowed someone's iPhone in order to update the firmware over it. This couldn't be more frustrating. And then a "Line 6 Expert" has zero idea what's going on? This is an embarrassment, truly. If I have to send this back, this will be the last Line 6 product I'll ever buy.