I have found that when I use RTE, my existing javascript edits do not get invoked.
I did some research to determine what exactly broke my already working code. It seems to be centered around the toolbar. As I slowly add elements from my production site over to a fresh test site, I tested the edits. They all worked until I copied the includes for the toolbar.
An existing edit that was working, now no longer displays the alert window. It also returns to the previous page instead of remaining on the page with the RTE so that the error can be corrected.
Needless to say, this is something that I did not expect.