After moving up to .NET 4.0 the following LINQ query fails to compile:

var allergies = from allergy in typedDataSet.allergy
where allergy.drug != string.Empty
select allergy;

I had to change the query to the following, using the Cast<> extension method to explicitly cast the allergy variable to IEnumerable<> generic sequence.

var allergies = from allergy in typedDataSet.allergy.Rows.Cast<TypedDataSet.allergyRow>()
where allergy.drug != string.Empty
select allergy;

Would it make any difference if I rebuilt the typed dataset in 4.0? Or is it the 4.0 compiler that is finicky?

I just created a new typed DataSet in .NET 4 and I can query it directly, without using Cast:

from row in new DataSet1().DataTable1
where row.DataColumn1 == "xyz"
select row.DataColumn2;

Could you try in a blank project with a new DataSet?
Also, what is the error message you are getting?