We're migrating a site from 4.62 to 5 R2 and today I ran into a problem that I can't see cause or solution for.
Basically, the migration tool fails with a duplicate key error, see log below: 

[1/26/2009 11:24:43 AM][Information] Finished migrating Object Store

[1/26/2009 11:24:43 AM][Information] Migrating database data...

[1/26/2009 11:24:57 AM][Information] Converting Custom Property's types and Assemblies...

[1/26/2009 11:24:57 AM][Information] Source C:\Program Files\EPiServer\MigrationTool\AutoGenerateCustomProperty.cs built into C:\EPiServer\Sites\Nito5\bin\AutoGenerateCustomProperty.dll successfully.

[1/26/2009 11:25:05 AM][Error] System.Data.SqlClient.SqlException: Violation of PRIMARY KEY constraint 'PK_tblAccess'. Cannot insert duplicate key in object 'dbo.tblAccess'.

The statement has been terminated.

at System.Data.SqlClient.SqlConnection.OnError(SqlException exception, Boolean breakConnection)

at System.Data.SqlClient.SqlInternalConnection.OnError(SqlException exception, Boolean breakConnection)

at System.Data.SqlClient.TdsParser.ThrowExceptionAndWarning(TdsParserStateObject stateObj)

at System.Data.SqlClient.TdsParser.Run(RunBehavior runBehavior, SqlCommand cmdHandler, SqlDataReader dataStream, BulkCopySimpleResultSet bulkCopyHandler, TdsParserStateObject stateObj)

at System.Data.SqlClient.SqlCommand.RunExecuteNonQueryTds(String methodName, Boolean async)

at System.Data.SqlClient.SqlCommand.InternalExecuteNonQuery(DbAsyncResult result, String methodName, Boolean sendToPipe)

at System.Data.SqlClient.SqlCommand.ExecuteNonQuery()

at EPiServer.Migration.SqlDataAccess.DeleteDomainPrefixFromTblAccessForUsers()

at EPiServer.Migration.MigrationWorkflow.MigrateDbData(Object sender, EventArgs e)

at System.Workflow.ComponentModel.Activity.RaiseEvent(DependencyProperty dependencyEvent, Object sender, EventArgs e)

at EPiServer.Migration.MigrationStepActivity.ExecuteHandler(Object sender, EventArgs e)

at System.Workflow.ComponentModel.Activity.RaiseEvent(DependencyProperty dependencyEvent, Object sender, EventArgs e)

at System.Workflow.Activities.CodeActivity.Execute(ActivityExecutionContext executionContext)

at System.Workflow.ComponentModel.ActivityExecutor`1.Execute(T activity, ActivityExecutionContext executionContext)

at System.Workflow.ComponentModel.ActivityExecutor`1.Execute(Activity activity, ActivityExecutionContext executionContext)

at System.Workflow.ComponentModel.ActivityExecutorOperation.Run(IWorkflowCoreRuntime workflowCoreRuntime)

at System.Workflow.Runtime.Scheduler.Run()