I've created working usb bootable windows installations with it at least 3 or 4 times.. i have one for the 32 bit and another for the 64 bit. I never saw any discussions about problems with it... and never had any problem booting up with it and running the install.
I'm wondering if the usb you are using has something on it that unetbootin doesn't remove when it writes? .. like a reserve partition. If it wasn't overwriting your bcd and bootmanager files it still would boot up the old way.
It is writing all the files from the iso ...right? Are you getting any error messages?
I usually format mine first to ntsf ... when I look at it from Fdisk it shows just one healthy, active, primary, partition