JDeveloper Migration and Customisation

Where I work we're trying to roll out a customised installation of JDeveloper. Customised in the sense that we've added some of our own code templates, set certain editor settings etc.
The problem I'm having is that we're rolling out 9.0.4 and when JDeveloper is started for the first time, it prompts the user to migrate their settings, which I find a bit odd because it's a virgin installation. Anyway, our code template customisations (in java.tpl) are getting lost i.e. JDeveloper uses the defaults. We've tried setting it up so that the files containing our customisations are copied over again after JDeveloper is started, but when we tried this we still got the migration message the next time JDeveloper is started.
Where is the flag that tells JDeveloper to perform the migration stored? Any suggestions as to how we can make this work?
Thanks.

After changing cables, swapping ports, running Applejack AUTO in deep clean mode, booting up with my hard drive that had not been updated with the "Migration and DVD/CD Sharing Update" (1.1)" and finally the Tiger Retail boot installation DVD, I finally gave up without solving the problem and shut down the computer.
After 2 more cups of coffee, I realized there was 1 thing I totally forgot to do. I remembered that I had not unplugged the computer from the outlet and held the reset button located near the battery on the motherboard.
You guessed it, everything is now working fine.
The only thing I can not figure out is why this happened after running the "Migration and DVD/CD Sharing Update" (1.1)". Go figure.
Bill

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