I am also unable to upload mzXML files using Windows 7. I tried to contact XCMS online via the submission form but apparently it is not working. Has anybody been able to solve this?
I also have the same problem. I am also unable to upload data files into the DataSet. I am using .mzXML files which are dragged to the "Drop Files Here" area and zipped automatically. However, when I press the "Upload" button, it appears the icon "Failed" in front of each file (yellow triangular icon with a black exclamation marker). I am using the latest Java, and added https://xcmsonline.scripps.edu to the exception site list in the Security tab in Java Control Panel.
I have also tried converting to .cdf and apparently uploads (an green icon with a white right sign appears on the side of each file), but the window doesn't close automatically and when I want to select the dataset I don't see any files uploaded...