I was having a similar issue. This is how it was resolved:
    Activate "File Download", True
    Connect "File Download", stWindows
    Wait 2
    Key "S"

    Activate "Save As", True  ' this to connect to the popup window
    sFilename = SmartDialog("Save As", "File name:<Editable text>").Value ' 
this gets and stores the file name to concatenate to the directory
    SmartDialog("Save As", "File name:<Editable text>").Value = 
"C:\Users\theuser\Documents\" & sFilename
    ' SmartDialog("Save As", "Save<Push button>").Click
    'SendKeys "%S", True ' Had to use sendkeys because key or enter would not 
work
    Enter ""
    Wait 0.2

    Activate "Download complete", True
    Connect "Download complete", stWindows
    Wait 2
    Enter ""

-----Original Message-----
From: [email protected] [mailto:[email protected]]
Sent: Thursday, March 07, 2013 4:40 PM
To: [email protected]
Subject: [talkbws] How to save excel file from a website

Hello,

I'm trying to save an excel file using the Web Save_File function to no avail. 
Instead, I'm forced to use click function to access the file. Then, IE throws a 
Save As pop-up window which I can't find in the Web Document List, thus unable 
to click OK to save. My question, how do I save the file by clicking on the 
save button? Or, am I using the Web Save_File function incorrectly?

Thanks,
Alice


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