The best option is to contact the company that developed the extension and ask them for help.
Probably, what is happening is that this extension needs to insert layout files and they did in the default theme, but not in your custom theme.
If you installed this count down extension manually (not using Magento connect) you have the folders and files, so you could take a look and check if is something like that:
If you find that, try to add this
your_extension.xml file in:
Again, this is just an idea. Since I don't know which extension you are using, my first approach would be to contact the company that made it because the problem can be more complex than just add files. Good luck!