Cool [Q] Beanstalk ROM Option Tweaks will not stick

I'm newly running the Beanstalk ROM 4.4.251 with great success. However, I have tried selecting the tweaks available under Beanstalk Options / Beanstalk Init.d scripts, and none will stick. One option titled, Enable Setrenice was selected as default and remains selected, but no others will stick once I leave that screen. I have updated to SuperSU via Titanium BU as a possible fix, but no luck.
Any suggestions?