The R-D1 has two settings for file numbering: Continuous and Reset (or something like that)
Continuous numbers the files continuously, regardless of formatting or other interference with the memory card.
The Reset numbers the files continuously, but resets to 000 each time that the card is removed and re-inserted. Therefore, the number might only show _002, but more than 2 images have been taken. Also, this causes there to be multiple _002 images to be created, leading to possible confusion in file organization.