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I think I've run into a bug on 0.3.7... When I tried switching a VRC6 tune to PAL mode I found that the 5 2A03/2A07 stayed in tune and the 3 VRC6 channels detuned. I was half-expecting detuning, but I thought it would either be all of the channels or none.
I have thought of a possible explanation though:
It could be that there is a PAL version of the 2A03 (the 2A07), but there isn't a PAL version of the VRC6 (what with it being Japan only).
I would imagine the 2A07 has different pitch tables so that it remains in tune when running at 50Hz whereas the VRC6 only has one set of pitch tables and therefore just goes flat.
If this is the case (and is deliberate) please disregard this.
I'm wondering if you actually need PAL mode with VRC6 enabled? This combination didn't exist back then, but I can see a reason to support it now as it's possible with a powerpak and a PAL NES. That is if it will be used.
(In earlier versions it actually worked in the tracker but exported files was forced to NTSC anyway.)