Well, I figured out what the problem is on looting/skinning/gathering, but it's in the internals of HonorBuddy, and we'll have to wait for them to fix it.
With my grindbot, HonorBuddy misses about 50% or more of the loots, and most of the skinning because of it.
If you examine the current POI while the bot is running, you can see that it sometimes goes straight from 'loot' to 'none', which skips skinning.
Sometimes it goes straight from 'kill' to 'none', which skips looting AND skinning.
Once in a while, it will loot. Even rarer, sometimes it will loot and skin.
You can modify this behavior by using a plugin like 'LootItAll' in the plugins section. This plugin checks every 3 seconds for stuff the grindbot overlooked, setting the POI when it finds it.
For stuff the bot would have missed, this is speedy and works well.
For stuff the bot would not have missed, it attempts to loot or skin a second time, and fails, taking up 10 extra seconds before clearing the current POI.
So - if you're out there to level and don't care about loot, don't use the plugin.
If you're out there mainly to loot and skin, use the plugin. Those intermittent extra 10 seconds are worth it, if it means you'll otherwise be leaving half or more of your gold behind.