I took a look at this. (It is frustrating; I know, as I've come across a similar layers problem.)
If you were using version 2.5, there's a screen flag for "Cycle Combos on Screen Init" that might fix the problem. Also, there's a few things with layers that could get the layers' combo cycling to work.
Since your quest is in 2.10, the only possible thing to do is find a way to use combo cycling on layer 0.
Would you consider having the floor be black instead of tile? That way at least the Gerudo could keep the same color and still use combo cycling. If your pallette for the Gerudo had the color of the light, you could add that to make a separate Gerudo sprite with the lit up background. You could still have the dark transparent layer and maybe leave a "hole" where it's not dark right over where the custom lit up combos are. That might work.
Edit: One other thing I just thought of (that might be a better solution) - just use colored floor combos to show where the Gerudo is looking rather than than using the overlay. You can either remove the darkness or just have the open hole as I suggested above.
To make the Gerudo sprite work, you could have the background of the Gerudo sprite part of the sprite itself. You could make floor tiles that use the Gerudo's CSet and use the "O" key in the tile editor (after using "C" to copy the Gerudo sprite, of course) to overlay the Gerudo sprites on top of them. (However, the "O" key only works for one tile at a time; if you copy more than one tile, it will only overlay the first copied tile over the first selected tile. But this shouldn't be a problem.)
This way, all your cycling is done with combo cycling, rather than relying on timing to make the animations line up.
Edited by Lightwulf, 03 December 2011 - 03:23 PM.