The scaffold calls the ExecuteJoinedDataset() method. It's hard to debug this because it's all encapsulated in subsonic, but from what I can tell, it's either a provider specific issue in GenerateWheres(), or it's the fact that parameters are never added to the QueryCommand object because the lines that do that are commented out in the ExecuteJoinedDataset() method of SqlQuery.cs.
So, first off, what provider are you using?