I am sorry that you are having problems with GenePattern. The error you are seeing is typically an issue with the GenePattern server and/or the browser and web application.
We have seen sporadic issues with people's files not uploading (to Amazon AWS S3) due to firewalls. Can you tell me if you are using GenePattern from within an institution or company network or from your own or home location? Also if you could tell me what browser and operating system you are using and your username I will look through our logs for other clues.
Thanks for your help and patience,
Ted