Are you doing Transformation before storing your data into QVD?
As far as am aware storing data into QVD shouldn't take 6 hours. As mentioned above you probably want to check the query you're using to extract the data from source.
My suggestion would be, extract the data as is (raw) and store it into QVD, i.e.
SELECT * //Or list of fields you want to extract
STORE DATA INTO .......DATA.QVD(QVD);
Then you can load the raw data and transform it as you which.
Hope this helps