Did you try changing value of
[android]
navigation_audio_stream=4
;0-STREAM_VOICE_CALL, 1-STREAM_SYSTEM, 2-STREAM_RING, 3-STREAM_MUSIC, 4-STREAM_ALARM, 5-STREAM_NOTIFICATION
Muting any specific notification in sys.txt will not solve problem as muting is caused by any sound generated by program.
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