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The audio performance of 0.3.6 seems to be different from 0.3.5. I never noticed any pops or audio buffering issues in 0.3.5, but it's very noticeable in 0.3.6. I have had to setup the buffer to 250ms or more to avoid it.
Using other applications, such as Live, also cause pops even when FamiTracker is idle.
I'm using a pair of M-Audio 2496 sound cards and am directing output to my main out (on my first card). This is the same setup in 0.3.5. I am using Windows 7 Professional (64-bit) as well.
I haven't done any major changes to the audio code in 0.3.6 so I'm not sure what's wrong, but I fixed a bug when using a custom refresh rate so I'll see if I did some mistake there. You haven't noticed any problems with other directsound applications?