Since I don't have an Ipad or Iphone, I'll make a wild guess.
What are the upload plugins you have activated? Three are available:
– uploader_flash: allows you to upload more than one file at a time. However, you need Flash and since Flash is not available on Ipads and Iphones (to my knowledge anyways), it won't work.
– uploader_jQuery: also allows you to upload more than one file at a time. However, it doesn't work with php < v.5.3
– uploader_http: the good old traditional, that works in all cases.
Assuming all options are available, one thing I don't know is how the setup is remembered. Is it once and for all or per user? If you set the upload options at home to flash and then access it through your Ipod, will it work? Or do you need to set it first to http on your home computer?