have you changed anything in the setup? try listening at lower volume levels.
perception of beats is determined both on time (attack and fall times) and freqeuncy (tonal pitch). severe clipping has compressive effects that distort both frequency and timing information, especially with closely spaced beats -- basically the next note starts before the current one has decayed enough, blending the two notes together. further, the attack of the next note is distorted, making it hard to determine as a distinct note.
sometimes a hole in the frequency response of a system will lead to some notes being heavily attenuated. in some cases a beat might seem to be missing -- especailly if a more favored note is being played at the same time.