Probably because you are trying to use file with channel positions that does not correspond to the EEG cap you used in your recordings, or because your acquisition software does not save correctly the electrode names.
To add the 3D positions to the electrodes, it is safer to match the data channels with the electrodes positions based on their names using the menu "Add EEG positions". If you use the menu "Import channel file", as you did before, it replaces channel names of the EDF file with the names from the file with the 3D positions, and there is nothing that checks this is appropriate. If you have no way to control that the order of the channels is the same in the two files, you should not use this option.
This might require that you rename all your channels manually in your EDF file (if you have multiple files, you can then copy-paste the modified channel file, you don't have to do the renaming manually for each file).
If you need additional help with this, please give us more information on your setup:
Where is this EDF file coming from? What acquisition software created it?
What EEG amplifiers and cap were used?
Where is your electrode position coming from? Are you using a template available in Brainstorm or real positions digitized on the head of the subject?