I am also new to SD cards and did some tests yesterday.
The new IDE's (apparently already since 1.6.8 or so) do have recognized problems with SD card operations and for me it seems that a lot of trial and error is currently going on to fix that issue. As a new project requires to have a SD card for data logging purposes on board I have to get the SD things function properly.
See my results and findings (so far) here and here.