JR,

 

There are several ways to change the retinal rivalry of the sky.  (At least you recognized that you had some).

 

You can adjust the hue (even in SPM).  Try going toward the purple shade until you don't see rivalry any longer with 3D glasses on.  As long as it's not too purple, it will still appear as a bluish shade through Red/Cyan 3D glasses.

 

Another method is to de-saturate an unfriendly anaglyph color such as Cyan, Blue, or Red.  You usually won't have to de-saturate it completely but just enough to reduce and/or eliminate the problem.  This can also be done via SPM, or another good friendly editor.  This method is generally what takes place if you use the "half color (red/cyan)" option in SPM.

 

I often use a combination of the two above methods.

 

Another alternative is to use some other options available in SPM such as the "Dubois (red/cyan)" feature, or "Gray Anaglyph" feature but that of course removes all color.  The Dubois feature is not bad unless there are people in the shot.  The feature makes them look greenish.  A way around that is to further adjust the greenish tint by de-saturating the green to an acceptable point.  I use IrfanView for this as one of the last steps before saving.  If you use IrfanView (freeware), make sure you have the option box checked for "Disable chroma color subsampling" if you're saving from there. 

 

Brian