Probably, as you have already said, it's because of the high CPU power needed for the decoding process. Try to raise BSplayer process priority in BSplayer preferences (CTRL+P -> General -> Process priority), set it to Above Normal, or High, and see if the player become more responsive (even if I doubt it since the same process is used to decode the stream and to parse the WinLIRC calls).
Or try to lower the player priority, maybe the commands can't be fully intherpreted by WinLIRC and sent to BSplayer
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