It could very well be that more XML edits or smali code to be more specific are needed to activate the CRT animation. The framework-res.apk recompiled fine so I'm surprised its causing issue for a basic one word XML change from "true" to "false" to enable the CRT animation.
The mod is common across Gingerbread.
framework-res.apk/res/values/bools/
Code:
<bool name="config_animateScreenLights">true</bool>
The true is changed to "false" to enable the CRT animation.
Only other thing I can think of is this is probably a "odex" file system which could be causing problems with recompiling without the odex file portion.