Ah, I understand. I've seen this problem before and was baffled by it too. The way I ended up fixing it was disabling the default Send-to-Excel on the chart and instead creating a macro that sent it to Excel and was triggered by a button. I then applied the formatting directly in Excel. I actually like this type of export better because it gives you more granular control over the output formatting. For example:
SET XLApp = CreateObject("Excel.Application")
XLApp.Visible = False
SET XLDoc = XLApp.Workbooks.Add
SET XLSheet = XLDoc.Worksheets(1)
XLSheet.Range("B1:B5").NumberFormat = "$#,##0.00;($#,##0.00)"
XLSheet.Range("C1:C5").NumberFormat = "#,##0"
XLApp.Visible = True
The problem is that I doubt this will work over AJAX so if that's a requirement, this solution won't help you.