magnus,
It seems that the 06.05.00.08 is what I have on all of my E versions for 6.3 SP1. So most likely the phone is fine at that version, but the 06.03.03.06 is most likely the version of firmware on the TFTP server for 6.2.5.80.
If you want you could force each phone to erase its firmware and download what is on the TFTP server, but most likely you won't have any issues with the phone.
Thanks,
TE