Reading and writing an SD Card with FAT16 or FAT32

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I have version 4.071 of the CCS compiler. I am using a PIC18LF2680 micro using the internal oscillator at 8MHz and running the chip at 3.3V. I am using the EX_FAT.c example provided in the CCS compiler example files. It includes the MMCSD.c file for an SD card interface. I have 20K pull-ups on all of the SD card pins. Here is what I have found. In FAT16 mode I can create files and directories and write and read the files in my application. When I install the card in a PC it doesn't see what I have done in the application. If I write a file from the PC to the card and put it in my application I can't see that file. If I format the card with the PC it erases the file the PC put on but my files still show up in my application and vice versa. In FAT32 mode I can't get it to consistently do anything. Can someone please help me out. I have tried a Fujifilm 256MB and Lexar 512MB card.