Hi Peter,
I was able to solve the problem by wrapping the NeatUpload inside a table like this inside SharedFilesModule.ascx:
<table class="fileupload" cellspacing="1" width="99%">
<tr>
<td class="fileupload">
<asp:Panel ID="pnlUpload" runat="server" DefaultButton="btnUpload" CssClass="settingrow uploadpanel">
<NeatUpload:MultiFile ID="multiFile" runat="server" UseFlashIfAvailable="true">
<portal:mojoButton ID="btnAddFile" Enabled="true" runat="server" />
</NeatUpload:MultiFile>
<portal:mojoButton ID="btnUpload" runat="server" Text="Upload" OnClick="btnUpload_Click" />
</asp:Panel>
</td>
</tr>
<tr>
<td class="fileupload">
<NeatUpload:ProgressBar ID="progressBar" runat="server">
<mp:SiteLabel ID="progresBarLabel" runat="server" ConfigKey="CheckProgressText" />
</NeatUpload:ProgressBar>
<GreyBoxUpload:GreyBoxProgressBar ID="gbProgressBar" runat="server" GreyBoxRoot="~/ClientScript/greybox">
<mp:SiteLabel ID="SiteLabel1" runat="server" ConfigKey="CheckProgressText"></mp:SiteLabel>
</GreyBoxUpload:GreyBoxProgressBar>
</td>
</tr>
</table>
With this solution, no changes are needed in the script.
Thanks for your help in diagnosing this problem.
Best,
Joe