Calling R::freeze() does not store any new data in the database (to my knowledge), how would a php script executed at a later date be aware that I called freeze() when I built the database? Should I be using freeze at the start of every one of my php scripts which use redbean?
Yes, it should be in the start of the script on every page that uses Redbean. I just reviewed the code, and there is no changes made anywhere that change it permanently. That being said, you have two options, at the start of every page, call R::freeze() -OR- edit rb.php around line 1380 and change private $isFrozen=false; to private $isFrozen=true;.