Yes this can be a problem, the rule is if a USB drive is present at boot up it will be sda and the internal HDD will be sdb. If there is no USB drive is present at boot up then the internal HDD will be sda and any USB drive plugged in later will be sdb. There are sometimes other ways to check which drive is which e.g. by checking the size of the drives, in my case the internal HDD is 500GB and the external only 30GB, but this can obviously have problems if the drives are the same size