This is not happening here.
I set a Dual Diatonic shifter to A Dorian, which is the 2nd mode of G major. All notes harmonize correctly:
A:C
B: D
C:E
D:F#
E:G
F#:A
G:B
I set a Dual Diatonic shifter to A Mixolydian, which is the 4th mode of D major. All notes harmonize correctly:
A:C#
B: D
C#:E
D:F#
E:G
F#:A
G:B
I also checked other keys and the quad diatonic shifter.
Factory Preset 319, Heavy Harmonies, provides a good testing ground.
Is your guitar out of tune? Is your unit's clock rate being forced to 44k?