You know how Gatherbuddy won't loot mobs when you're a Druid? I think it's because there's a special speed optimization in place to make herbing go faster, but it's probably applying that speed to the looting to, which is BAD! It doesn't wait even half a second for the looting to occur, before it goes off to the next waypoint... then it comes back to the mob, does it again, and again, and again. This makes you look like a bot, and makes one reluctant to use the 'Loot Mobs' feature of Gatherbuddy, at all... but without that turned on, you won't get motes of harmony! So - I've been using Grind Bot lately. But the main disadvantage of THAT bot over Gatherbuddy, is it always starts at the beginning of the profile. So if you have a continent-wide profile, it will run across the ENTIRE continent, ignoring your waypoints, to get to the first waypoint. Soo... what I've been doing lately, is starting the Grind Bot profile hotspots near the teleporter, because what's the first thing you do upon hitting Pandaria? Hit the 'run' button on your bot. This way, at least it's not running across the continent to get to the first waypoint, it only takes a few steps.
Turn on the game's Auto Loot option, and the game loots it for you as soon as the loot window opens. If the bot tries to loot it just gives some error spam about item being busy. Also what is your ping to home/world? My theory is that is has sometime to do with lag or maybe lag spikes.