I had thee exact same problem, Raven. And so did someone else I know. We at first did the work-around that you did (rezip the file and reload the template). And, like you, we knew that it wasn't our FTP program causing the problems. For us it turned out to be the webhost. We had to ask them to look at the Templates folder and set the permissions for us -- don't ask me why, but for some reason it just wasn't sticking with our ftp programs. Once they did that, we were able to drag and drop the individual image or css files into the template folder without having to hassle with reloading the template file. So, I would recommend talking to your webhost on this one...
Hope that helps
