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We just got a news from our developers that this issue has been resolved. Could you try the following and see if you were able to download the submissions as excel file.
1. Log out and log back in to your JotForm account
Could you also try downloading the submissions using this method: http://www.jotform.com/help/101-How-to-create-an-Excel-Report.
Do let us know if the problem still persist after the suggested solutions above.