I have had a little success so I'm writing this to aid future users.
There is a technical buggette with the upgrade process to 5.0. If there is zero config the upgrade fails as described above. If you go through the initial config then the upgrade works. For some reason the last part of the upgrade does not work if you perform it from a factory install.
Therefore the working path to a v5 IDP from a factory install is:
1) Factory reset using USB/CD
2) login to IDP and run through initial script giving basic IP info
3) upgrade to 4.1r3
4) delete v4 install file and reboot
5) upgrade to 5.0
If you fail to perform step 2 in the process then it will fail.
Ian