In ColdFusion, the # is a reserved character. To escape it, you'll have to double them up to escape them:
<cfset format.dataformat = "##,######0.00">
Silly that they didn't account for this either in the documentation or followed ColdFusion's formatting rules using 9s instead of #s.
Here is my full working standalone test code:
<cfset myQuery = QueryNew('number')>
<cfset newRow = QueryAddRow(MyQuery, 2)>
<cfset temp = QuerySetCell(myQuery, "number", "349348394", 1)>
<cfset temp = QuerySetCell(myQuery, "number", "10000000", 2)>
<cfscript>
//Use an absolute path for the files. --->
theDir=GetDirectoryFromPath(GetCurrentTemplatePath());
theFile=theDir & "getTestInv.xls";
//Create an empty ColdFusion spreadsheet object. --->
theSheet = SpreadsheetNew("invoicesData");
//Populate the object with a query. --->
SpreadsheetAddRows(theSheet,myQuery,1,1);
</cfscript>
<cfset format = StructNew()>
<cfset format.dataformat = "##,######0.00">
<cfset SpreadsheetFormatColumn(theSheet,format,1)>
<cfspreadsheet action="write" filename="#theFile#" name="theSheet" sheetname="theSheet" overwrite=true>