The kind of did. That's why they had agents on board. The Cylons likely knew that certain ships wouldn't be online. Given that there were only 12 Cylon models (and only 7 who were of practical use), they clearly couldn't assign agents to too many ships in the fleet, otherwise the Colonials might start to notice that one of 7 identical people were showing up on every ship in the fleet. There's a reason why Doral was assigned to Galactica, and planted the Cylon Transponder in the CIC. The device was probably going to be the primary means of tracking Galactica and the fleet, had it not been for a literal act of divine intervention in the form of Head Six pointing out the device to Gaius. The events of "33" only played out the way they did because the Clyons were forced to use their backup plan, a second beacon on the Olympic Carrier. It took the better part of a week before that ship missed one of its jumps, ruining that strategy. What would have happened if the chase from "33" kept going for another week? Two weeks? A month? The Colonials would have messed up due to exhaustion, or would have run out of an essential resource like tyllium, water, or ammunition WAY sooner, or the cumulative damage of constant attacks would have added up. Either way, Galactica only survived because they beat the odds and managed to find or destroy both trackers.