[HansW]

instead of writing all that, just post your gathering profile .lua file. I'll have a look. We know about the Bug that sometimes the skillmanager adding skills in strange chars. If that happens, just reload the lua modules, that should fix it. As for your other Problems, i assume you just have a different understanding of how the skillmanager works than it actualy does. To call that a bug is a little strange. I've used the skillmanager on all crafting and gathering jobs without any problems. It's also possible that what you are trying to archive is simply not possible with the way it works. But since you seem to be unable to just describe in a simple way what skill you want used at what time, its pretty hard to give you proper support on the issue.
It would help if you could just write bullet list of the skill you want to use under what condtion. Just the list, not what's not working and what you tried to setup.