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I got help by Episerver support on this one. Posting the answer if someone else comes across the same problem.
When upgrading to cms 6 existing xforms-data is migrated to dynamic datastore. To do that the site is initialized and in this case imagevault was installed and caused an error on the initialization. (probably because the installed version of imagevault wasn't compatible with cms6)
So the following was done to upgrade:
1. Remove ImageVault dll's from the bin folder
2. Upgrade to cms 6
3. Upgrade to cms 6 R2
4. Put the imagevault dlls back into bin folder.
Im trying to upgrade a site from CMS 5.2.375.236 to cms 6.0.530 but Deployment Center doesn't succed. I get the following error: