In normal 2D mode the GPU tryes to converse energy (and run cooler), so it does actually underclock your GPU in normal desktop mode. It's just normal. The 2D mode is so much easier to GPU than 3D mode, where all speed is needed!
As i said. Try some some gams and try to see if there are artefacts or any other anomalies to check out how your card can take those owerclockking ghanges. One alternate would be using some GPU test like 3Dmark. They show to you yours GPU's real speeds in 3D mode.