Hi, I also have a VA3.
This also happens to me, but I understand why it happens.
Every instrument, Saxophone, Clarinet, Guitar, Flute etc. have different pitch ranges. The notes that that particular instrument can use may only range to high octaves, for other instruments it could be lower. So what your VA-3 does, is it makes an octave shift, depending on what instrument you select, when you go into Arranger mode.
You'll find eventually that it's a good feature. It will take a bit of getting used to at first, but it doesn't bother me anymore.
I hope this helps
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