It can be caused by several different things in my experience.
1) A cable issue when using external speakers. Try using a different TRS 1/8" cable (a stereo patch cable).
2) Some sound cards come equipped with features for 5.1 and 7.1 surround sound. Sometimes after an update, these settings are turned on. If you have a two-speaker system you might be receiving signals not designed to go to those speakers and you hear a muffled sound. The solution is to drill down into your sound card/system settings and "turn off" these enhanced setting (ie. Dolby, 5.1, surround sound etc.).
3) The playback/recording frequency is set incorrectly. Try changing the recording frequency to 16 kHz or 24kHz (the two most common) and see if the problem goes away. Sometimes the frequency is just incompatible with your system.
4) Reboot.