That is odd that it isn't creating a blank worksheet even with the append flag. I tested exporting using the Excel 97+(Monarch V9) setting with regular reports we use as I don't do that much with PDF's and did not have anything to test with and it did create sheets with headers. Normally I use the Excel 97 + (Monarch V8) export setting.
Have you tried doing the same thing using Excel 97+(Monarch V8) export setting instead?
Give that a try.