I found the problem... some dlls were missing from my project and the migration wasn't able to load some librairies to perform the upgrade.
I had the same problem. I still had EPiServer 4 and 5 installations on the machine from the upgrade process. I uninstalled all EPiServer programs and re-installed just EPiServer 6, and it worked.
I tried to upgrade several demo site and everything went well during upgrade. There is one site that was at the latest version of CMS 5, as the others.
The thing is when I run Upgrade site from the deployment center on this site I get the following error:
An unhandled error has occured:
Cannot resolve dependencies for the following module(s)
At C:\Program Files (x86)\EPiServer\CMS\6.0.530.0\Upgrade\System Scripts\Migrate Data (SqlServer).ps1:95 char:27
+ Set-EPiLongStringSettings <<<< -DestinationDirectory $wizard.SelectedApplication.PhysicalPath