There is a problem with USB3 options, when using loader / tools, using serial (USB) i.MX bootloader(s).
For example, some MFG problems relate to the general USB3 support under OS and issues may be solved,
when USB3 ports are disabled in Win 7 / 8. Please try to disable USB3 if possible.
I expect MFG tool, supporting USB3, will be published soon.
In meantime You may try one of preliminary (non-published) MFG release, supporting USB3.
Let me know if needed.