after about 30 mins of troubleshooting this is what I figured out about this profile.
1. First, you have to save the file in profession buddy as mentioned. E.g. extract the profiles folder into the profiles folder within profession buddy, next place the sub-folder contents "HBProfiles" into the Professionbuddy HBProfiles sub-folder.
2. When starting the bot it will need to be updated to the new pandaria levels. The files in the Mining folder are all set to max level 86 and needs to be changed. simply open in text editor, change (level 91) and save.
3. The files use a combination of different bots, so if your guy is just flying around and not mining you need to change the settings inside gatherbuddy2. Make sure that mineral harvesting is checked on both gatherbuddy and under settings and tools on the main GUI of honorbuddy.
Hope this helps, if I run into anything else I'll repost.