Commented Issue: EF4.3.1 on .NET 4 / VS2012 - The mapping of CLR type to EDM type is ambiguous because multiple CLR types match the EDM type [596]

We're using EF 4.3.1 code-first under .NET 4.0 and VS2012. We have a query that looks similar to the following:

ctx.Set<Entities.A>().Select(a => new DTO.A { Id = a.Id, Name = a.Name }).ToArray();

Entities.A is defined in an assembly called Entities and DTO.A is defined in an assembly called DTO. Under VS2010 EF 4.3 this worked fine, but under EF 5.0 it throws the following exception:

Schema specified is not valid. Errors:
The mapping of CLR type to EDM type is ambiguous because multiple CLR types match the EDM type 'A'. Previously found CLR type 'Entities.A', newly found CLR type 'DTO.A'.

Stack trace is

at System.Data.Metadata.Edm.ObjectItemCollection.LoadAssemblyFromCache(ObjectItemCollection objectItemCollection, Assembly assembly, Boolean loadReferencedAssemblies, EdmItemCollection edmItemCollection, Action'1 logLoadMessage)
at System.Data.Metadata.Edm.ObjectItemCollection.ImplicitLoadAssemblyForType(Type type, EdmItemCollection edmItemCollection)
at System.Data.Metadata.Edm.MetadataWorkspace.ImplicitLoadAssemblyForType(Type type, Assembly callingAssembly)
at System.Data.Objects.ELinq.ExpressionConverter.TryGetValueLayerType(Type linqType, TypeUsage& type)
at System.Data.Objects.ELinq.ExpressionConverter.GetCastTargetType(TypeUsage fromType, Type toClrType, Type fromClrType, Boolean preserveCastForDateTime)
at System.Data.Objects.ELinq.ExpressionConverter.CreateCastExpression(DbExpression source, Type toClrType, Type fromClrType)
at System.Data.Objects.ELinq.ExpressionConverter.ConvertTranslator.TranslateUnary(ExpressionConverter parent, UnaryExpression unary, DbExpression operand)
at System.Data.Objects.ELinq.ExpressionConverter.UnaryTranslator.TypedTranslate(ExpressionConverter parent, UnaryExpression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TypedTranslator`1.Translate(ExpressionConverter parent, Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateExpression(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.UnaryTranslator.TypedTranslate(ExpressionConverter parent, UnaryExpression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TypedTranslator`1.Translate(ExpressionConverter parent, Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateExpression(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.MemberInitTranslator.TypedTranslate(ExpressionConverter parent, MemberInitExpression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TypedTranslator`1.Translate(ExpressionConverter parent, Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateExpression(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateLambda(LambdaExpression lambda, DbExpression input)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateLambda(LambdaExpression lambda, DbExpression input, DbExpressionBinding& binding)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.OneLambdaTranslator.Translate(ExpressionConverter parent, MethodCallExpression call, DbExpression& source, DbExpressionBinding& sourceBinding, DbExpression& lambda)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.SelectTranslator.Translate(ExpressionConverter parent, MethodCallExpression call)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.SequenceMethodTranslator.Translate(ExpressionConverter parent, MethodCallExpression call, SequenceMethod sequenceMethod)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.TypedTranslate(ExpressionConverter parent, MethodCallExpression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TypedTranslator`1.Translate(ExpressionConverter parent, Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateExpression(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.MemberInitTranslator.TypedTranslate(ExpressionConverter parent, MemberInitExpression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TypedTranslator`1.Translate(ExpressionConverter parent, Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateExpression(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateLambda(LambdaExpression lambda, DbExpression input)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateLambda(LambdaExpression lambda, DbExpression input, DbExpressionBinding& binding)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.OneLambdaTranslator.Translate(ExpressionConverter parent, MethodCallExpression call, DbExpression& source, DbExpressionBinding& sourceBinding, DbExpression& lambda)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.SelectTranslator.Translate(ExpressionConverter parent, MethodCallExpression call)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.SequenceMethodTranslator.Translate(ExpressionConverter parent, MethodCallExpression call, SequenceMethod sequenceMethod)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.TypedTranslate(ExpressionConverter parent, MethodCallExpression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TypedTranslator`1.Translate(ExpressionConverter parent, Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateExpression(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateSet(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.UnarySequenceMethodTranslator.Translate(ExpressionConverter parent, MethodCallExpression call)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.SequenceMethodTranslator.Translate(ExpressionConverter parent, MethodCallExpression call, SequenceMethod sequenceMethod)
at System.Data.Objects.ELinq.ExpressionConverter.MethodCallTranslator.TypedTranslate(ExpressionConverter parent, MethodCallExpression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TypedTranslator`1.Translate(ExpressionConverter parent, Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.TranslateExpression(Expression linq)
at System.Data.Objects.ELinq.ExpressionConverter.Convert()
at System.Data.Objects.ELinq.ELinqQueryState.GetExecutionPlan(Nullable`1 forMergeOption)
at System.Data.Objects.ObjectQuery`1.GetResults(Nullable`1 forMergeOption)

I'd understand the problem if the types were in the same assembly (a long documented issue with EF whereby it cannot disambiguate using just the entity name), but from a different assembly?

Is this a regression, it used to work...?
Comments: Sorry for the delay; somewhat typically I'm unable to reproduce this outside of the solution we stumbled upon it in the first place. I need to isolate what the actual difference between my unit test and the real solution is. I'll try and post something on Monday.