I have created a specific layout for home page as you said.
now when I upgrade from version 1.0.4 to version 1.0.5 the header color is default not only for home page, but for all the pages of the website.
I have done a rollback for the moment, but you can connect on admin area, make a template upgrade to version 1.0.5 and check pages. you will see that header is not transparent.