Here are a few other factors that can play a role:
1. Winds, east vs. west bound
2. Actual distance flown -- especially in Europe, with both standard and tactical restrictions, the distance can vary quite a bit directionally on a city pair
3. Speed flown (late outbound but OK
return? Restricted by ATC in one direction?)
4. Altitude flown (either intentionally for speed purposes, or due to ATC restrictions or weather)
5. Maneuvering on approach (or even departure) -- for traffic or other issues, can make a big difference, also early descent/leveloff into some airports can be severe and others nonexistent, runways can make a difference (e.g. if both airports have 09 active, eastbound flight can be much shorter than westbound, depending on the arrivals/departures for the specific airports)
Also did you count the taxi burns as well? Were the taxi times similar?
Big thing is knowing the actual distance, speed, and altitude for each direction.