Bump! We had the very same problem yesterday. Have not yet found a solution.

I've filed it as a ticket with the developer support. Hopefully they'll have some answers.

This is now solved!

The culpit was the EPiServer.Packaging.Patch1 version 2.1.90.0 that was residing in the wwwroot\modulesbin.

I removed it and ran it again without that specific error. In my case I had the ImageVault CTP in place which also interfrered with the VPP Migration Tool. I manually uninstalled the Add-On and now it ran successfully without any errors.

After re-adding the add-on and the EPiServer.Packaging.Patch1 version 2.1.90.0, the site seems to work as expected with the VPP's migrated.

Tobias how did uninstall ImageVault?
If you removed ImageVault was the site functional after this? How did VPP-tool manage to execute under that scenario?

All I did was removing the plugin from wwwroot\modulesbin. Ran the VPP-migration tool and then re-added the plugin afterwards. So the site might not be fully functional while running the migration tool, but that was not an issue for me since the site was not used at the time of migration.

Ok thanks Tobias, this I have already tried. I removed the ImageVault.EPiServer7.AddOn.dll from modulesBin and the ImageVault dll:s that resides in bin folder (4 items in ImageVault 4.5.120). Removed the dependency in web.config to ImageVault. Runned IIS-Reset, the VPP-migrationtool still gives me same error.

I have also tried to remove all assemblies from bin and replaced those with with the binaries which are installed on a vanilla 7.5 CMS version. Seems like I'm missing some configuration (according to the error) that screams "Give me ImageVault!", also removed any references added to ImageVault.

Log from VPP Migrationtool

Could not load file or assembly 'ImageVault.EPiServer7' or one of its dependencies. The system cannot find the file specified.

at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoad(String assemblyString, Evidence assemblySecurity, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean forIntrospection)
at System.Reflection.RuntimeAssembly.InternalLoad(String assemblyString, Evidence assemblySecurity, StackCrawlMark& stackMark, Boolean forIntrospection)
at System.Reflection.Assembly.Load(String assemblyString)
at EPiServer.Shell.Modules.ModuleFinder.LoadAssemblies(IEnumerable`1 configuredAssemblyNames, VirtualDirectory moduleDirectory, ShellModuleManifest manifest, AutoDiscoveryLevel discoveryMode)
at EPiServer.Shell.Modules.ModuleFinder.GetModuleInDirectory(String routeBasePath, String moduleResourcePath, IEnumerable`1 configuredAssemblyNames, AutoDiscoveryLevel discoveryMode, String configuredName)
at EPiServer.Shell.Modules.ModuleFinder.GetModulesInSubdirectories(String rootPath, AutoDiscoveryLevel discoveryMode)
at EPiServer.Packaging.Utility.PackagingModuleProvider.GetModules()
at System.Linq.Enumerable.<SelectManyIterator>d__14`2.MoveNext()
at System.Collections.Generic.List`1..ctor(IEnumerable`1 collection)
at System.Linq.Enumerable.ToList[TSource](IEnumerable`1 source)
at EPiServer.Shell.Modules.ShellModule.MergeDuplicateModules(IEnumerable`1 modules)
at EPiServer.Shell.ShellInitialization.Initialize(InitializationEngine context)
at EPiServer.Framework.Initialization.ModuleNode.Execute(Action a, String key)
at EPiServer.Framework.Initialization.InitializationEngine.InitializeModules()
at EPiServer.Framework.Initialization.InitializationEngine.Initialize(HostType hostType)
at EPiServer.Framework.Initialization.InitializationModule.Initialize(HostType hostType)
at EPiServer.Framework.Initialization.InitializationModule.FrameworkInitialization(HostType hostType)
at VppMigrationTool.Util.SiteProxy.InitalizeEPiServer(String webConfigPath) in d:\Builds\132\EPiServerCMS Modules\VppMigrationTool\Sources\C\TFS\VppMigrationTool\Util\SiteProxy.cs:line 52
at VppMigrationTool.Util.SiteProxy.Initialize(String destinationPath, String virtualDirectory) in d:\Builds\132\EPiServerCMS Modules\VppMigrationTool\Sources\C\TFS\VppMigrationTool\Util\SiteProxy.cs:line 129
at VppMigrationTool.Util.SiteProxy.Initialize(String destinationPath, String virtualDirectory)
at VppMigrationTool.Converter.get_RuntimeProxyWrapper() in d:\Builds\132\EPiServerCMS Modules\VppMigrationTool\Sources\C\TFS\VppMigrationTool\Converter.cs:line 52
at VppMigrationTool.Converter.FillSiteData() in d:\Builds\132\EPiServerCMS Modules\VppMigrationTool\Sources\C\TFS\VppMigrationTool\Converter.cs:line 101

I don't think you need to remove the references to ImageVault from the project itself. I did not. Just remove the add-on from modulesbin.