Ok, I'm home and can check HB now. What I'm referring to is this:
Once you open Wow and then start HB, make sure you have the profile you want to use selected and then select the bot that works for that profile - I'm guessing Grind Bot or Gatherbuddy2. In either case, once you select that, click the Settings & Tools button. You need to check the Advanced Mode to see the options I'm referring to. Once you select Advanced Mode, in the middle 2nd row you'll see a group title Looting. Make sure Loot Mobs and Skin Mobs is selected. To make sure you're getting all the mobs in the area, you probably want to select Kill Between Hotspots and may have to adjust the pull distance. I have found in some areas that 40-45 works well.
Hopefully that will get skinning working for you.
Have fun,
'Al'