Zach,
Thanks. I found that if I remove and re-insert my SD card that the flushes to the SD card file system work always. It seems that the actual flush or write to the SD card does not occur after I reboot with the SD card inserted.
The most confusing part is that I can run the HTTP Server and FileSystem examples and have no problem after a reboot.
It also seems that my problem has gotten worse as I finished my application, it seems that something along the way broke. I just don't understand why re-inserting the SD card makes everything work as expected, but on reboot power or soft reboot, it won't work as expected.
Any ideas or thoughts are appreciated.