If you notice a bit of "uncooked flour taste" then you have uncooked flour.
And, Zereh is right on track! After you saute you veges - add the flour and cook for 2-3 minutes, stirring very frequently, before you add liquid. You don't want the temp very high - you don't want to brown the flour. Lower the heat before you add the flour to Med or Med-Low - or just move the pan off and on the burner (30-secs on - 30-secs off) while you stir.
When you add your liquid - add it slowly and whisk like crazy to prevent lumps. Then bring the temp up to a boil, and reduce to a simmer for 2-3 minutes.