Bootanimation can't be changed anymore for unknown reason
I had a similar problem on CyanogenMod and it turned out to be broken permissions. I tried the following which worked in the shell only for whatever reason. You need to be rooted and have ADB installed. The following commands mount the system partition for reading and writing, copy stock bootanimation zip (change location, or skip), copy custom bootanimation zip to data/local, and (re)applies correct permissions to media folder and zip files, and finally reboot (if you want).

adb shell
su
mount -o remount,rw /system
cp /sdcard/download/cm/bootanimation.zip /system/media
cp /sdcard/download/bootanimation.zip /data/local
chmod 775 /system/media
chmod 644 /system/media/bootanimation.zip
chmod 644 /data/local/bootanimation.zip
reboot


If you want to restore to stock, simply delete the data/local version. If you want a new one, replace it while keeping the system/media version intact. You can also create your own bootanimation using this guide from XDA.