I'm not sure what update you have, but you can't update from 2002 to 2003 A05 with just the 2003 update if you have the one I think you do, I think the update was meant for people with A04 to update to A05, however you can bypass this with the bootloader method.
Basically you need a cf card formatted and the R64365, read the whole thread it will help you out...
This is the link you are looking for
Problem with upgrading PPC2002 -> 2003 - Axim Users Dot Com
I've done this successfully, but you want to be careful as you can brick your X5, if it doesn't go right..fortunately none of my flashing adventures have ended up badly so far..knock on wood..