Answer is explained here: https://stackoverflow.com/a/14074407/645495
From here: http://code.google.com/p/android/issues/detail?id=38282
All phones using MTP instead of USB Mass storage do not properly show the list of files when that phone is connected to a computer using a USB cable. Android apps running on the device also cannot see these files.
This affects files written using Java APIs, but does not appear to affect files written using the C API.
The solution is to reboot the device.