It's because the design (at least initially) called for five engines:
http://scifi.stackexchange.com/questions/16526/etymology-of-the-name-quinjet
The diagram at the bottom labels 4 of the engines, and the big, unlabeled afterburner at the center makes 5.
Now the TV series ride has bad placement of the back two jets http://up-ship.com/blog/?p=21589
The original quinjet dated back to the John Buscema days, but that refined late 70s version probably originated with Perez or Byrne.
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