The reason the leading zeros are removed is because the file was opened with Excel and then saved without the leading zeros.
Excel removes all leading zeros unless the cell is formatted as a 'Text' cell.
Excel does not save 'Text' formatting on the csv format easily.
So, in order to keep leading zero from disappearing in Timekeeper ID, you need to open the file in any text editor, like Notepad or Notepad++.
Found a related article regarding this issue here.