In order to "Log and transfer" the FS-100 footage into FCP, you need to make sure that the original file structure of the card is kept intact.
If you're transferring directly from the card itself, there should be no issues at all.
If you're copying cards to hard disks for transferring later, make sure you create a folder that represents each individual card, then copy the entire contents of that card into its corresponding folder which you just created. If you grab just the media files from it and copy those over, FCP will not be able to read them. It needs the original file structure to read them.
The Log and Transfer function with the FS100's AVCHD footage works like a charm, it transcodes 4-5x faster than DSLR footage does through the same process. I absolutely love it.
One note. If you recorded your footage in 1080p60, it will not read it. FCP does not support 1080 60p. You will have to use another 3rd party software like Clip Wrap to re-wrap the files so Compressor can then use them and convert them into 30p so FCP can utilize them.