You seem to be affected by the USB device detection bug holvoeth mentioned.
It seems to be affecting some devices (USB sticks from a given brand, namely Sandisk) more than other ones, there are a couple workarounds that you could try integrating in your script, either reset the USB bus or rename the slot, see:
http://forum.mikrotik.com/t/rb5009-routeros-7-9-1-usb-slot-keeps-changing/167185/1
http://forum.mikrotik.com/t/usb-disk-issue-after-hardware-reboot/172598/1