When you have more skills than what the in-game skills section can 'afford', so to speak, there'll be skills that won't be visible in the window. And, while there's an option to remove skills that you can't use at that moment, if you have too many skills you can use, the problem persists.
My suggestions are a couple, all aiming to alleviate the above issue:
* Make the skills section scroll down based on the cursor's current position. This will let players see all of their skills without issues.
* Move toggeable skills and racials to a section of their own. Players seeking to re-read what some of these passives do can refer to that section, but this won't fix the issue in the given case that you still have too many skills.
...Or anything else anyone may come up with and provide in this thread. It's honestly been an issue for quite a while, and it'd be cool if it could be fixed.