I think I have worked out and solved my distortion problems with 2.0b3 and 2.0b7
I was very puzzled that other people had no problems with the MP3 file I posted, so I looked into what was happening a little more. I had already checked that my loudness was at 0dB and that I had my volume set at under 0dB.
I never use the equaliser, so I hadn't though to look in there. When I had a look at the equaliser settings I had a shock. Instead of the first bank of (flat) settings being selected the second bank was selected and they weren't flat. The left channel was flat, but the right channel had seven of the ten bands set to minimum (none of the bands were boosted at all). I changed the equaliser to use the first (flat) bank of settings instead and tried one of my test tracks, sure enough the distortion had gone.
The unit clearly wasn't using the eq settings that the interface showed it as using, I WOULD have noticed if the right channel had it's output pulled down that much. I have since gone back and selected the second set of settings again and it sounds as it should, with the right channel very obviously attenuated across much of the frequency range.
So, it looks like what probably happened is that as part of the 1.03 - 2.0b3 upgrade process (or sometime after that) the eq settings got corrupted in some way that was causing the player to boost the output signal beyond 0dB, thus causing clipping on some tracks.
Also the corruption was not causing 1.03 a problem, when I downgraded to 1.03 the problem went away, until I went back to 2.0b3 or 2.0b7
So if anyone has unexpected problems with clipping then go check your equaliser and switch to another (flat) bank of settings just in case you don't have the settings you think you have...
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Remind me to change my signature to something more interesting someday