That issue may be connected to the USB storage device you are using, as an example some SanDisk USB sticks tend to cause the issue (the RoS is confused whether the device is USB2 or USB3.,x) see:
http://forum.mikrotik.com/t/usb1-vs-usb2-mount-after-each-reboot-a-surprise/182437/1
http://forum.mikrotik.com/t/usb-disk-issue-after-hardware-reboot/172598/1