>I suggested that my manager discuss the issue with the CEO
Point blank:
Why not tell your manager you already spoke with the CEO instead of
1. Not mentioning you already overstepped your manager
2. And the skip-level boss/CEO liked the idea.
This seems like potentially good intentions being easily perceived by your manager as passive-aggressive. Maybe your skip level told you to use that phrasing.
Regardless, good luck.
I think you're misinterpreting the situation, because I didn't "overstep" my manager, and in a small company everyone has a relationship with everyone. (IE, what I did was taking initiative and making good use of dead time.)
I'm not comfortable discussing this further in a public forum at this point, but you're welcome to look at my profile to contact me directly if you want to.