Right now, silence becomes permanent to anyone who happened to be within the area of effect, whether they were the direct target, or if they step outside the 20' radius. Unless something is the direct target of silence (in which case saves and spell resistance comes into play), then they are only silenced for as long as they remain within 20' of the target point. This is a major issue for spellcaster-heavy parties (like mine), because a single spell cast early in the fight can mean disaster (like just a few seconds ago... poor, poor Luther the Wizard).
Looks like it's a result of the occasional case where some spell effects just become permanent and we don't know why. Use Liv's mod and talk to Jaroo, ask him for resurrection, then ask him to remove a permanent spell effect from your character. While investigating the spell, though, I did notice that it doesn't allow a save if targeted directly on a person. I have changed the script to allow a directly targeted creature to save and negate the spell completely. That way, if an enemy casts it on your character, your character has a chance to be totally unaffected (thus, no radius, and no silencing of the rest of your party). This is per the SRD. Will include in my next spell package update, which should arrive as soon as I finish one last tweak to Warp Wood.
I wasn't entirely clear, I think. The effect wasn't permanent, it just stayed with my characters for 60 rounds even when I had left the area of effect.
That is an unfortunate artifact of how the engine handles the spell. It places a silence condition on anyone who comes within the radius of the effect, and it gives that condition the same duration as the base spell. Thus, if you fail your save on an area silence, you're basically hosed. It's not correct by the SRD but would require a .dll hack to fix.