Basically, if you are using FS-100 without a P2 card, you will need to set the TC on the HVX200 to Free Run mode when shooting 24p (Rec Run TC will not work). You will also need to set the USER BIT setting to FRM RATE. When FCP imports the P2 files, it requires these settings to remove the unused frames.
If you have a P2 card inserted (even if you are not recording to it), this issue does not appear to occur.