I can't remember if the fakenative setting is it or not, but some Googling myself has produced mention of an env variable - ENV:Picasso96/AmigaVideo. It seems that setting this to different values changes the chipset timing. I'd have a look and see what you have in there...
Edit: According to the AHI documentation, this would normally be set to 31KHz to enable sample rates through Paula of 48KHz - I'd bet that's set on your machine!