So I first noticed this when switching classes using the Skill Saver system and couldn't use one of my skills for some reason. After switching around a few times, I ended up with negative skill points and some of my skills were unavailable for use even though it showed that they were spec'd and ready.
To start off, I chose the starting point to be the class that I was already spec'd in. This is the same class and setup as my first Skill Saver profile.
everything is normal at this point and all skills are usable.
I then move to switch to my second profile, and already before actually switching, I can see it showing a -13 skill point result and having 31 skills spec'd in.
after switching, the case remains the same.
However, upon going to character select and back in, we see a different situation.
As you can see, the difference in number of skills spec'd in the image above and the image below is 13! (all of songcraft, frigid tracks from Scorc, and skewered from Vit)
Before relogging, the skills that were "not really spec'd" were un-usable by the character
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relogging shows the skills that were actually spec'd and were able to be used.
*should be noted that using the skill saver to switch into gypsy again would result in the -13 skill points situation once more.
From Gypsy, if I switched back to Cleric, my first Skill Saver profile and our starting point, it results in having -24 skill points.
and upon relogging after that switch, I get
once again, the difference in the number of skills shown to be spec'd and actually spec'd is the negative skill number.
switching out all 3 skill trees to something that isnt part of any of my skill profiles results in something fun, having only 4 skill points to work with.
But if I go from relogging as a cleric and switching into one of the other trees I save saved in one of my profiles, the skills come automatically spec'd in already
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and this resulted in having 36 skills spec'd and -8 points. The skills that aren't "really spec'd" can't be used.
So one of my theories is that the Skill Saver saves 6 different skill trees and only shows you 3 while allotting your points into the other 3.
The other is that it holds onto the first skill set you save, mine being Shaman (sorcery, witchcraft, vitalism) in Skill Saver profile 1 which explains why sorcery and witchcraft already came spec'd when I switched to them.
My current solution to all this is to manually spec the skills when I log back in and only use a Nui or skill manager to switch around. Using the skill saver starts messing it up again