When an Encore project has had numerous (which for Encore can be only 1 ) errors, simply making a change may not be enough. To test specific possible issues, start a brand new project, with a new name, and use only what you need to test the problem. And in your case, if you haven't already, I would start the project from scratch. You can import the psd menus.
Either way it shouldn't make the build not work.
I assume that it could make the build not work, particularly if the problem is the menu as you stated.
See this for menu duration and timing issues.
The short audio will play and stop. The video will probably set the duration of the menu.
the build stops while rendering a menu now.
What happens if you use the "Render Motion Menu" option.
Edit: File -> Render -> Motion Menus.