Let me simplify this:
Start
All timing mats/antenna must be behind the starting line (primary and back up). As previously mentioned the software will take the last transponder read - nearest to the starting line.
Finish
All timing mats/antenna must be beyond the finish.
Some timers still don't understand this concept but as a measurer it is very clear. If the start mats are place after the starting line there is always the chance that the transponder will be read on a short course!