Conditionals Break the JS on my site

If I add any Conditionals to my webform, any custom (theme) javascript I have written on the website, that isn't separately wrapped in a jQuery(document).ready(function($) will not work.

I have used the Zen scripts.js default page to run all of my custom scripts—so may of them are not wrapped in a Doc Ready Function, and I already tried wrapping all my scripts this way, one-by-one, but it of course breaks some.

Firebug also gives my zero help, as no errors show in the console.

Is anyone or has anyone experienced anything similar. I have never had a conflict like this in quite a while... was hoping someone had a quick solution.