I was posting a comment on a pick and an explanation came to me.
In the very first episode JD suggests that there is a penny jammed in the door that Janitor is fixing. When it turns out there is, Janitor assumes it was Jd and has played pranks on him ever since as payback.

It all started with a penny...

Late in the show, we hear JD only has two fears: sharks, and some wierd thing with pennies.
NOw we all know JD is a sensitive guy- could the torment that Janitor has given him have caused this strange penny phobia???