When I use the compare file utility and sync up my files, Toad seems to change some formatting in the file. This causes issues for me when viewing it in Programmers File Editor, another file editor program. When I view it in this editor, the formatting has changed and there are characters now added to the beginning of the file. Also, some files have doubled in size.
View the file in the Toad editor, Notepad, or Wordpad.
Waiting for fix to be released in a future version of Toad for Oracle.