Some Android phones have their internal memory split into two blocks.
One is used for the internal or / folder. The other part of the internal memory is returned by getExternalStorageDirectory(). This is still internal memory from user and/or PC side. But for Android it is external memory.
So probably you are looking in the wrong folder.
For example in my Samsung S4 I have:
/
/storage/emulated/0
/storage/extSdCard
"/storage/emulated/0" is returned from getExternalStorageDirectory(), while "/storage/extSdCard" is my external SD card.