Make sure the Blu-ray software is internally decoding all lossless and lossy audio soundtracks to 2.0 LPCM if you have a 2.0 speaker setup on your computer. Or do up to a 7.1 LPCM decoding for 7.1 computer speaker setups. Try connecting a A/V receiver to the graphics card HDMI output and selecting bitstream to see if the audio problem goes away.
I have actually seen Blu-ray audio problems go away on an old year 2007 Laptop computer when the graphics card driver is updated to the latest version. Also install the latest Windows updates. You might need a software update to your Blu-ray player, but since the problem is happening only on the internal BD-ROM drive and not the external, this might be a problem with the internal BD-ROM drive since the problem goes away when using the external BD-ROM drive.
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