Thanks. Thanks to Martin we know this bug seems to have been introduced for him in v2.6.30-rc1 (more precisely: ALSA: hda - Use digital beep for AD codecs, 2009-02-06). I suspect it may have been fixed on at least some systems by v2.6.35-rc1~478^2~1^2~24^2~3 (ALSA: hda-intel - AD1984 thinkpad - add analog beep input control, 2010-03-26). But that is only a wild guess. Could you test with the kernel from testing, sid, or experimental?
It works correctly for me with kernel from testing (2.6.38-2-amd64). Thanks. Petr