Do not export your site into the files folder of your design file!!!
The files folder of your design file, in this case called "countdown_web_files" contains files that will be automatically placed in your htm_files folder on every export. It contains the flash and gif files that you have in your placeholders for example. But you can also add any custom files and subfolders to it and all this will be exported along with your site on every export.
Now as you export your site into this folder, the next time you do export, the previously exported site is placed into the files folder of the exported site. And so on.
This is not the bug. It is expected to work this way. You just have to know what "countdown_web_files" folder is there for and how it works (explained in help).