I mean that since I can't figure out what application is making the sound, the only thing I can think of is to turn off sound entirely. It's not a speaker or sound system problem, it's just some signal from the server that I don't know the meaning of.
I thought it may be an apache server error, or an LDAP login error, or something. Only server apps are running, no user apps. Also it's more of a "THUuuuuuunnk, thuunk". There's actually only two syllables in the sound.
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John