I got this issue a lot when my web browser (Safari for Mac) saw that these were zip files and insisted on putting .zip on the end (making it .pk3.zip) when in fact I wanted .pk3. It was quite a pain to remove because a simple rename just made it assume I wanted to hide the extension instead of actually changing it. If you are on a mac, you'll need to use the Get Info window to rename the file, and it should ask you if you are sure you want to change the extension. You do. On anything else, use whatever methods you can to ensure the full filename ends in .pk3 and then drop it as-is into the base folder.
Failing that, use Firefox to download it :)
All problems = solved with firefox