Well, I have netduinos that have been 100% erased, including sometimes the bootloader being replaced, many times. I have one hooked up right now that is "factory fresh" with no messing about at all. And I have tried lots of things in between, including most all the pre-release software images. The first one I got has the little erase pad about worn out!Have you tried this technique to reset ?
I am uncertain exactly what that linked procedure is trying to do. I am suspecting the board doesn't need reflashed or erased, it is working fine. The problem is Visual Studio under VirtualBox hangs between the deploy and entering the debugger, apparently due to some kind of failed handshake with the Netduino, but that is a guess. Jacking the board allows it to go into the debugger and things proceed from there.
To date, most of my Netduino time has been running FreeRTOS on the little things. But I wanted to get back to trying the C#/.NET stuff and maybe learn something. So far, using VS in VirtualBox has resulted in a less than reliable development cycle. I am sure there are very few of us, wanting to use VirtualBox under Linux...
EDIT: I should also point out that this is functioning well enough to do development, it is just an additional step is needed to jack the board.