Since you're starting v3 with a v3-prelude domain without upgrading first, v3 should see that it's a prelude domain and perform the upgrade. Did you see some text like this when you started the domain? "Domain needs to be upgraded before it can be started. Attempting upgrade now..."
If not, there may be a bug that prelude domains aren't automatically detected. However, the normal path would be to run the upgrade tool on your domain before using it with v3.
If you find any errors in your log at all, you can add them to this issue:
https://glassfish.dev.java.net/issues/show_bug.cgi?id=9752
But check to make sure the domain was upgraded first as described above.
Thanks,
Bobby
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