I have just downloaded 2.1 Final and am having a similar problem.
SubSonic.SqlQuery q = new Select().From<Northwind.OrderDetail>
.InnerJoin<Northwind.Product>
.Where(Northwind.Product.CategoryIdColumn).IsEqualTo(5);
(This is not the exact code, I don't have Northwind installed, but illustrates my problem)
As far a I can tell, if the column is not in a From table, the NullReferenceException is fired.
I tracked the offending line down to ANSISqlGenerator.cs Line: 230. The FindColumn method returns null.
Unfortunately I do not have enough knowledge of subsonics innards to fix the problem.