Ok, here's my take on this...
Fact
When sound is digitized into something like a wave file, there is an x number of data pieces taken which hold the info about the sound at that very movent. This is called the frequency of a wave file, because the frequency number is the number of times each second that a data piece, called a sample is taken. For CD quality music, this is about 44100 hz (aka 44.1 khz). Freespace 2's sound files mostly use 22050 hz.
My guess, based on the code
Freespace 2 uses a sound system which fades in between different loaded music files when an event occurs. An enemy ship warps in, for example. To make this *sound* right, it needs to know when it can fade out the file rather than just fading it indiscriminately.
So, each song in Freespace 2 is divided up into measures. At the beginning or end of a measure, Freespace 2 will fade to a different song if it's needed.
This means that to set the two variables correctly, samples_per_measure must be set to the number of samples per section of music. num_measures is the total number of sections for the music file.
So say you had a simple drumbeat - abaab - that was 2 seconds long, recorded at 22050 hz, repeating over a 30 second music file. To find the number of samples per measure, you would use the equation (frequency * measure time) or in this case (22050 * 2). To find the number of measures, you would use the equation (music time / measure time) or (30 / 2)