The A-90EX (with VE-RD1) is 64-Voice polyphonic. A 2-Part performance should rarely have voicing problems unless you are using a LOT of piano chording with damper.
The 'arpeggiation' problem sounds like you have a MIDI delay/loop occuring. If you are playing back a specific MIDI score, try temporarily disconnecting the A-90's MIDI Out to the PC and see if it stops.
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