How to avoid losing custom CSS/JS on a form using Ctools Modal when Validation Errors Occur
Turns out that the JS and CSS files were not being dropped, but since the modal window uses ajax, all the ID's were being incremented when the form was rebuilt after a validation error. 

So JS and CSS selectors such as edit-field-act-property-ref

&lt;div id="edit-field-act-property-ref"&gt;


would become 

&lt;div id="edit-field-act-property-ref--1"&gt;


which is a problem if you have CSS/JS targeting the original. I thought I would share in case this helps out somebody else in the future.