It's not major but still an issue I guess.
After your settings ini file is created for the bot itself, not necessarily character setting's files.
The skills in the main settings ini file didn't have Clan Skills learned when i first used it. Due to the fact none of my characters are in a clan.
After logging onto a character that does have clan skills the skills weren't automatically updated.
My route around this is to extract the skill data from the setting ini file from a new complete set up bot settings.ini file. To do this I had to copy the folder and delete any files except the exe. Reason I did this is so I wouldn't have to go back and learn all my current data and retype my logins. This way I can just go down to the skills in the new ini file and copy/paste them over to my old settings ini file. In which I'm hoping they will show up in the skill list.
So if my alternative is a complicated and difficult way please let me know. Or if there's something I'm missing.
(NVM ... Just added them to my esper bar and it recognized them)