The instructions for apiguard say to apply the second treatment 2 weeks after the first application.
My observations of hive behavior during treatments would seem to indicate that there are 3-4 days at the beginning when the treatment is pretty highly concentrated and causes a lot of bearding compared to untreated hives. I am making the (possibly incorrect) assumption that the maximum effect on mite health also happens during this time, and tapers off. After 2 weeks there is either nothing left of the treatment or it is completely encased in propolis - either way no longer having any apparent effect.
So, for some period of time (3-5 days I guess) the phoretic mites that would enter capped brood are either killed or compromised as well as any mites exiting the brood. So that would leave a few days worth of mites inside of capped brood when the treatment starts that exit after it is much less effective - and are therefore not effected.
So why not repeat the treatment in 4-5 days instead of 2 weeks? One answer is that it is less stressful on the bees to give them a break. Another possibility is that apiguard usually causes the queen to stop laying for a few days (it does) and the 2 week timing takes advantage of that... hadn't thought of that until just now, but it still seems like 2 weeks would be too long.