It appears this issue cleared itself though no idea how/why; I'm curious if anyone else has seen it.
I created a dataflow from a SQL DB and for the initial set of tables it worked pretty much fine first time. I came to add a new query to another table and while it seemed to read the table OK, when I've created some steps in the query it reported that my flow contained 'untyped data'. And yet every column has a data type. it's been presenting the error for the last 2 days of attempting to get it working and then I get an error when trying to load the query (although it actually does add it because its still there when I browse back to the dataflow page, and recovers from the cache).
Suddenly today it seems to have worked without issue. Ayone aware of why this might have happened in case I can avoid issues in future?