As you can see in this part, java do not have problems to access pulse:
index: 99
        driver: <protocol-native.c>
        flags: START_CORKED 
        state: CORKED
        sink: 0 <alsa_output.pci-0000_00_1b.0.analog-stereo>
        volume: 0: 100%
                0: 0.00 dB
                balance 0.00
        muted: no
        current latency: 0.00 ms
        requested latency: 113.38 ms
        sample spec: s16le 1ch 11025Hz
        channel map: mono
                     Mono
        resample method: speex-float-1
        module: 8
        client: 87 <Java>
        properties:
                media.name = "Audio Stream"
                application.name = "Java"
                native-protocol.peer = "UNIX socket client"
                native-protocol.version = "16"
                application.process.id = "26076"
                application.process.user = "ant1"
                application.process.host = "ants"
                application.process.binary = "java"
                window.x11.display = ":0.0"
                application.language = "en_US.UTF-8"
                application.process.machine_id = 
"0b5a826cfe1ab9dd2bb7c9444a89694a"
                application.process.session_id = 
"0b5a826cfe1ab9dd2bb7c9444a89694a-1262064218.846503-57789871"
                module-stream-restore.id = "sink-input-by-application-name:Java"

Do you have any problems with  mplayer? i so it in your list.
Is it possible that your java application some how hardwired with alsa?
The problem is, if you set java to use alsa, it will still use pulse
with alsa2pulse plugin, which has problems too.

-- 
Sound does not work with openjdk
https://bugs.launchpad.net/bugs/491784
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