I can only guesstimate that the D700 and the D300 made two separate folders on the same card due to them being two separate cameras and when placed in the D700 for formatting it did not or could not format the D300 folder. So once you placed it into the D300 for formatting, only then was it able to format the remaining data.....
Anyone?
Try a test using the same card in both cameras and do some test shooting with both cameras, then place the card in a card reader and view it from your computer to see if indeed there are two separate folders from each camera. Then try formatting them again..... See what happens.