CLM 6.0.1 How Can I Disable Theme Validation?

I have a theme that works great in 5.0.2. Now we are upgrading to 6.0.1 and I am trying to deploy the same theme. There seems to be some kind of validation occurring on the JavaScript which prevents me from uploading it to the application. Is there a way to disable the theme validation in 6.0.1? I know the theme works, I just need CLM to allow me to upload it.

The 6.0.1 error message that blocks me from uploading my theme says:

Error uploading theme .zip file: TypeError: doc.getElementsByTagName(...)[0] is undefined. ID CRJAZ1516E

Oddly, I do have a couple of "document.getElementById" statements in my JavaScript, but I don't have any statements that look exactly like the error message.

Has theming changed in some appreciable way in 6.X?

Edit: It sounds like this is a problem on the server side and not a problem with the theme that I am trying to upload. Stack Overflow has examples of other people who have seen the same error. It seems to be related to JavaScript trying to access a node before the node is defined. My JavaScript in my theme doesn't have that problem because it specifically catches it in a try block and retries until it succeeds. So there must be some sort of wrapper JavaScript that CLM is executing behind-the-scenes.