Irish customs will stamp your VAT refund form if you check the goods you plan to export from the EU in your baggage in DUB. German customs in FRA will only certify exports of goods you have with you (in your handluggage). Lines at the customs office in FRA are long, and they are very particular about seeing the good you are asking them to certify.

Once the form is stamped you can collect the refund from the global blue office in the terminal, lines in front of that counter are also rather long. So I would advise you to get the form stamped in DUB before departure to FRA.