What alters the efficiency of (cantilever) brakes?
I have had similar problems in the past, and I would group them in these "categories":


Your rims are different. One of them has a smoother surface, or a different alloy, or a different quality alloy, and the actual friction is lower in one of the rims. I have this problem currently with one of my bikes;
One pair of brake pads is different. It can be from a different batch, or different model, or different brand, or different material, etc.;
If your pads are the (very common) asymmetric type, THEY SHOULD ALWAYS HAVE THE LONGER SIDE POINTING BACKWARDS! Everytime you brake, the pads tend to rotate "outwards", pulled by the moving rim, and that's why it's always best to assemble the pads with the longer side pointing backwards;
One or both of your brake bosses (and overall bike structure) flex when you brake. Specially on the front, where the "rotating outwards" can combine with the (carbon?) fork "opening" while braking. This is very successfully solved with a (somewhat infamous) "brake booster";
There are some possible geometric tunings, but this specific model doesn't seem to allow for tuning the pad position or the straddle cable length. If that were the case, attaching the pads away from the brake arms (thus widening the angle between the arms) and increasing the angle of the straddle cable gives the best mechanical advantage;
The pads have not burned in yet. Going for a tough ride, with long descents and possibly some dirt, could allow the braking power to emerge;
The braking surfaces keep being contamined by some non-cycling-related influence in your house: car exhaust near the front wheel, use of some spray product near the bike, oil coming from some wierd place, etc.


I hope this helps!