Your question was a little confused by asking about the Timy. I am not an S4 expert, but if set-up correctly (you MUST have a printer connected to the S4 to time a FIS race or USSA for that matter) you should get something like marking before starts and finishes. I think it is KZ and ST but I am not sure. It won't print bibs or net times.
Are you missing starts or finishes? Is it a cable issue (loose wire)? Do you have the min time set and/or delay set? There are a nunber of ways to determine where these starts and finishes are not registering, starting with a printer attached to the S4 that you can read, even if you have to hand mark it, is a start. If you know, as you seem to, the S4 is printing the starts and finishes, go to the next step and see for sure it is sending them out and not ignoring them somewhere before the DIN port. If it is sending then, is it a cable issues? Next would be a computer serial port problem or possible a buffering issue. Finally I would look at Split Second as the culprit.
Good luck!
Jenna