I've noticed this one ever since I had the machine. Some new files show up on the web interface, others don't. Its quite random, and they are sensible file names too, i.e. no spaces and not excessively long.
Doesn't make any difference whether you reload/reboot etc.
I keep meaning to see if any of the entries that don't show have something in common.
Some directories don't show either, even though they are created.

As an example it doesn't like "GearsetSpinner", but it will accept "gearset-spinner"

Firmware: Reprap 2.0(RTOS)
WifiServer: 1.21RC4(08b3)
Web interface: 1.21.1