The Source Monitor is a simple player (as is the tiny player window in the Project Panel), and plays directly from the AV file on the HDD, where the Program Monitor is displaying from the Timeline, and takes into consideration any decompression, any Effects, etc.. There are also several settings in the Program Monitor, that can affect the display, such as Quality (try on Highest), and whether one is displaying 1/2, 1/4, etc. Resolution. What are all of the settings in your Program Monitor.
Also, what form of MPE do you have enabled, and what is the make/model of your video card? At the same time, you might want to list your video driver number/date.
If your sequence is interlaced, the program monitor display will be interlaced
whereas the AE file, and hence the source monitor is not.
Good points that I had not thought of.