Hmmm. I know the M2 example files on the SD card have the "wipe at the beginning" sequence. I always wanted my files from Creator to do that, and they only did after I specifically added a "wipe" sequence to the Start G-code. (I think it's on the misc. tab...). I took ketil's starting and ending G-code adders that he posted here some time ago as my basis and tweaked from there.
Now the way my start G-code works (and it's executed after the machine homes and the temperatures stabilize) is to move Y to about 30 to get around the binder clips holding the glass on my M2, move X over to just past the right edge, extrude some filament, then go back to X=0. There my custom start G-code ends and the G-code from the slicer takes over.
For my custom end G-code, I turn off the heaters, move Z +20mm relative to drop the bed a bit, back out the filament (-50mm extrude), move Y to about 50, then slowly move X back and forth between 25 and 175, with the 50mm fan at about 180(/255), for about a minute to cool the part. Then I move Y to about 230 to "present" the part and turn off the fans and motors (at which point the bed drops). This works great for unattended prints -- leaves everything cool and the filament ready to pop back in the bag with the desiccant.
Sounds like you may have imported somebody's .FFF file or loaded somebody's .factory file, then saved the .FFF -- which it uses next time, I think.
I keep copies of my start and end G-code in a text file on the desktop, just in case I need to recover them.
Hope this helps.