Does the same problem occur if you browse to the home page in the subweb then select the IE File menu and choose Edit with FrontPage?

If all else fails you could open the main web on the server, right-click the subweb folder and choose convert to folder. It would then become part of your main web and you could re-publish from your computer and reconvert the folder to a subweb again. Whether you would want to do this would depend on what you have in your subweb. A unique subweb theme, for example, may very well be deleted when you convert back to a folder.