It doesn't matter whether you are using the developer or production edition of FileUpEE. The only way to download multiple files at once is to use a rich client like our XFileEE ActiveX control. This is because the HTTP protocol doesn't provide a way to download more than one file in a single HTTP response. XFileEE makes it appear to the user as if they are downloading multiple files in one step, but behind the scenes it is making a separate request for each file.
FileUpEE includes samples that show you how to download multilple files with XFileEE. Please let me know if this answers your questions.
This means something went wrong with the server-side code. Are you using our samples or your own code? If you are able to get our samples working, I suggest using them as a model.