Why does my micro SD usb show that I no longer have files on it, but the files are still there on the DS?

I have an r4, and with it came the micro SD usb 2.0. Also the memory card, with 2 GB of mem. When plugged into my computer, it shows that I have certain games that don't show on my DS and lack the ones I have previously deleted. When plugged into my DS, I still have games that I have previously deleted and still do not have games that I have recently downloaded. It used to work and I have the new r4 update... why is it not working now?