Allen, If you're importing the .gpl file, I'm assuming you're using Generic Import. Try loading the map into Site Mate and then Export it as a Shape File (in Site Mate). Then try loading the Shape File into Farm Site and see if all the data is there. The key is that if Site Mate loses GPS while logging, it will stop the file and then automatically restart it and start logging. You don't notice anything, but it adds a "Stop" and a "Start" in the .gpl file. Normally when you import these files with Generic Import it will give you some error messages that there are lines without valid GPS coordinates. When this happens you should have the option to stop or continue. I have a feeling that this may be why you're not getting all the data.
If this isn't the problem, try making sure that you have a blank PC Card that you're logging to or one that has plenty of free space.