>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.