With newer ChampionChip systems (manufactured after 2001) you can expect 100% reads for everyone in a road race. Of course at the finishline, a few runners (1 or 2 out of every 1000 finishers) might only be read by the backup system, which is the second set of mats you cross at the finishline. But between the main and back-up lines at a road race, these systems will read everyone. However, that accuracy is not acceptable for cross country.
When using a ChampionChip system to time a cross country race, each runner needs to have two chips - one on each foot. With two chips on for each runner, you can expect all athletes to be read on the primary system (first set of mats). If only one chip is used per runner in an XC race, the main line will most likely miss athletes - unfortunately there are some timers out there that allow this.
For cross country, a photofinish system needs to be used to verify all finishers. (in case of close finishes and in case an athlete does not remember to wear their chips) The use of both a chip system and FinishLynx is powerful and a very efficient way of timing cross country. But, let me emphasize that the entire race needs to be reviewed by the photofinish system. Since the chip data can be downloaded instantly, this process for 250-300 runners does not take long. Unfortunately, the NCAA D1 committee does not follow this procedure and that's why they've run into trouble at NCAA D1's.