I think he is using the wrong script for Auto ZipAlign. The one by Wes Garner points to system/apps which is already zipaligned. All new apps are installed at data/apps and hence the log show no new apps zip aligned.Once again DookMatt, your auto-zipalign is incorrectly implemented, it's not working.
Also, you don't need to mount system for changing default frequency and governor.
Need to modify the script a wee bit to point to data/apps. You can make the following changes to the zipalign script
Change this: for apk in /system/sd/app/*.apk
to: for apk in /data/app/*.apk
Not too sure it's the right way but works alright.
** I have not checked your ROM. Based on Noejn's comment and the fact that you mentioned it's Wes Garner's script.
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