I have very little experience with pectin, but after glancing at some of gel cheat-sheets it looks like your problem might be syneresis, which is science talk for weeping. Pectin weeps (and then you, too, weep). Some gelling agents are more susceptible than others. It just means they eventually let some water break out of the hydrocolloid matrix. Pectin supposedly has less syneresis with the addition of calcium; someone here can probably tell you what form to use and how to use it.
Additionally, there are other gelling agents that are much more stable. I'm not sure which ones best mimic pectin (or if you'd be interested in other textural properties). It may be possible to stabilize agar with locust bean gum (agar by itself has serious syneresis issues). Possibly also a gel with locust bean gum and iota carrageenan.
