Hmmm, it seems as if you are constructing scales incorrectly, though I'm not exactly sure where the problem lies. If you play a G mixolydian scale, you are playing G A B C D E F, as G mixolydian uses all the notes from the C major scale. Note that as the G major scale normally has an F#, when you flatten that you get an F, not an Fb. You never have a scale that has the same note twice, even if they are called different things. Remember that keys other than C major have sharps or flats in them; for instance, G has an F#, and D has both an F# and a C#. This is so the intervals stay the same. The intervals of a major scale is Tone, Tone, Semitone, Tone, Tone Tone, Semitone. That is, a tone from C to D, a tone from D to E, a semitone form E to F, etc. If you number the intervals in a major scale, you get 1,2,3,4,5,6,7, upon which all other scales are based. A mixolydian scale has 1,2,3,4,5,6,b7. However, that doesn't mean that the seventh note is necessarily flat, but flattened form what it was. If you have the G scale, you flatten the F# to an F, not make the F note a flat. Is this where your problem lies.
Hope this helps.