Other (Non U.S.)
Almost, but not quite. It's not certain scenarios, but always. It's used to remind you that the resources in that country still belong to the Jihadists until the end of turn. This prevents the US from "stealing" the victory from the Jihadists just by doing a last minute regime change. See the "NOTE" on page 6.
NOTE: Via 2.3, green Regime Change markers prevent an easy last-turn reversal of Islamist victory. If the current turn is unlikely to be the last (3.3) and you wish to avoid the step of flipping the marker (5.2.9), place it tan side up.
I think I've never used that green/tan marker, I've just always put it the tan side up, but then again, I've never been in the situation where that would've mattered.