Good spot. I have both version like you (3.9 and am testing the Beta release, but I think the Beta version is treated as a completely separate installation) - I see / hear the same. Definitely a little audio glitch at the beginning of existing sequences. Also, making a new sequence in 3.9 with audio only (no effects), I get the same audio glitch issue.
I don't have my display hooked up (hey, it is September), but agree the on-screen preview looks a little out of sync. I played one of my sequences with super-tight timing marks back at very slow speed, I agree the audio seems slightly ahead of the preview graphic. I assume the preview graphic represents what's being output data-wise at that point in time, but don't have anything connected to confirm.
I'm not using OpenGL in my case.
I'm also finding the 'back to start' button unreliable
I also bumped into the audio->speed/tempo option which I've not come across before, which seems to switch how the audio plays back if not at 100% speed - i.e. whether it pitch shifts or not. NicePersonally I prefer the 'off' mode which is equivalent to speeding up / slowing down a tape/vinyl playback.
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