Ok, with a fresh head I started working on this again, and I started with MsTimer2. If I completely remove the library, my 3 Serial.println's all match.
This is odd, as I was using the ::stop, and ::start functions of MsTimer2 so I guess the actual setup of the system.
Whats a trailer queen? This is for a push bike, I just want the rear red LED's to flash at around 3Hz, which is well within any UK laws regarding additional bike lights.