I just looked into this issue and have fixed it in my copy so it will be fixed in the next release.
In the meantime there is a workaround that also solves in my test.
If you edit the file with a text editor /SharedFiles/SharedFilesModule.ascx
look for this:
<portal:jQueryFileUpload ID="uploader" runat="server" />
<portal:mojoButton ID="btnUpload2" runat="server" Text="Upload" OnClick="btnUpload_Click" EnableViewState="false" />
currently it is inside an updatepanel, but this kind of file upload can only work with full postback not with ajaxpostback of the updatepanel.
So you need to move it from where it is to below the closing tag of the updatepanel.
Hope that helps,