Mike,
I’ll contact you offline as well, but these are the proper settings for both HVX and FS-100 for fixing the problems you are having. Place the HVX in UB Mode FRM Rate, 1394 Control Ext, 1394 Cmd Sel Rec_P, TC-rec run. Place the Firestore in External Ctl Pause, TC ext, non-drop Frame. With these settings, the FS-100 is triggered everytime you hit the record button on the HVX, and goes into record pause when you hit the HVX record button again, just like it would if you were using a Mini DV camera tape. Using these settings I have never had the problem you mentioned while recording.