Thanks for the kind feedback, Avery!
Yes, "Flicker Free" is a misnomer. What I actually do is blend 2 frames together (this frame and the previous frame). With a limit of only 6 objects (Player 0/1, Missile 0/1, Ball and Background) some programmers would take to drawing certain objects every other frame. This causes flicker... On a real TV this gets somewhat blended by the fact that the phosphor on old TVs took a fraction of a second to dissipate and so that soft glow would help reduce the flicker (though, believe me, we still had to deal with the flicker!).
Flicker Free attempts to blend every other frame - and to do so as fast as possible this is a simple OR operation. The logs floating on the water are drawn every other frame... and the "holes" in the logs are drawn as blue on odd frames... and when those are blended together, the log turns blueish.
Some games are almost unplayable without Flicker Free mode. Yars Revenge is one such game where the large shield surrounding the enemy is done in 2 big blocks which flicker out of existence on modern monitors. The Atari Greatest Hits had this problem.
I choose to enable Flicker Free for a few games that really need it. Frogger is boderline... it's playable without for sure. The Official Frogger doesn't have it enabled by default (although it does flicker) mainly because there just isn't enough CPU power to render that complex game with the FF blending.
Such is life with simple blending. The new versions of Stella on the PC have amazing rendering engines that can emulate the time decay of phosphor akin to the old TV screens. But that requires processing power... and we just don't have enough of it on our beloved little NDS handheld.
So yes, you can turn off Flicker Free mode and get the right colors... and a bit of flicker. Or use Flicker Free and get more solid looking objects that tint wrong.
At least until someone smarter than me can improve upon my flicker free algorithm