I found the problem and it's nothing to do with DBLinq. I had been testing some stuff out from IronRuby and within that there is an assembly called Microsoft.Scripting.Core which duplicates the System.Data.Linq namespace (why it does that I don't know). With a reference to the Microsoft.Scripting.Core assembly my test DBLinq app would compile and run fine but would have the where clause missing on the SQL. Removing the assembly reference resulted in the where clause correctly being generated.
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