OWA Advanced Customization Template - Password Change

From looking at the customization template, I would say that the most likely reason you're seeing this type of experience is because the logon.inc page was completely overridden instead of augmented to fit the OWA style.

The original template contains code to build the change password fields dynamically when necessary, but the customization template manually specifies the username/password fields instead of letting the APM build the form within the customized style of an OWA page.

To fix that, you will probably need to get a copy of the original logon.inc (you could create a new logon page and copy it from there), and then go through the code there to figure out how to customize the page in such a way that you let the PHP code generate the page as it needs to but you wrap that in your own customizations.

I'm working on doing this same thing with my own custom table/style on the login page, and it's tedious, but it works.

Hope this helps.