i noticed the issue also in firefox. when i click a download link, it comes up as index.php, but it is actually the proper file, so just right click and save as, rename to <whatever>.rar/zip and your'e set. i don't think i had the issue in chrome at all.
so when it prompts to save the "index.php", its not the actual index.php, but the actual correct file to download. damn you firefox!