There are at least two issues here:
One, we do not have USB working in user programs yet. I absolutely understand the value of this feature and the product sucks without it, but this is only temporary. There is a lot more we want to do with the software and this is one major feature we are working hard on, but we chose not to hold up hardware delivery on software issues. Anyway, the USB issue is in development. When we ported Arduino to Flutter pretty much everything from the Due carried over pretty easily... except the USB portion requires a full rewrite. Luckily we have some skilled community developers on the issue and I am in contact with another developer now who has been writing the USB code for this, so I will be testing that soon.
Two, thank you for the detailed bug report for windows. It sounds like there's at least one issue here, potentially two. We know that auto reset is not working and that is very frustrating I'm sure. I haven't looked at that in detail yet but it is high priority for me.
I'm glad programming seems to be working now for some of you.
So what is the current status for you all? Has anyone been unable to get it working? Is anyone still struggling to get the basic programming working? @Flutterman is it still inconsistent for you?