Pausing bitstreaming is always a bit of an issue, because the AVR loses the bitstream sync no matter what you do, and specifically in DirectShow as well, because the audio decoder doesn't really control any of that. The renderer might still be buffering data, so even if the decoder tries to reset the bitstream on un-pause, there is no guarantee that it would work.
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LAV Filters - open source ffmpeg based media splitter and decoders
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