Not really sure what to say. Which way are the fans facing? What is the orientation of the GPU to these fans? What kind of fans does the GPU have?
GPUs fans are intakes, ie blowing towards the card, so for best results those fans should be blowing in towards the card. If they are set as exhaust then they might hurt things a little. Depends on the general airflow of the case. As long as fresh air is getting to the GPUs intakes and the heated air is exhausted from the case at some point it should be fine.