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Custom - as in, MP3s I've put onto the USB storage. I'm not sure if it's true with the pre-installed ones. Do you experience it with the pre-install ones? Luckily it's easy to recreate, so I'll test it now. I can recreate the issue by plugging/unplugging the USB storage, or rebooting the phone - after both these actions, the phone always changes the assigned ringtones.
By the way, this issue was reported to Google here: http://code.google.com/p/android/issues/detail?id=13413. Anyone who is experiencing random ringtone changes, please visit the link and star it so more attention is brought to Google; hopefully which will get fixed in a future update.
Will report back in a second regarding the pre-installed ones.