Take off the apron and see if the 2nd position switch in the trough is closing somehow.
Also check the 2nd ball lock switch.
I recently had an odd problem when 1 ball was locked the coil would sometimes all of a sudden kick the locked ball out while shooting the next ball around.
It was fixed by replacing the intermittently working 1st ball lock switch.

I had the exact same problem till lunch today:

http://pinside.com/pinball/forum/topic/whirlwind-keeps-kicking-out-two-balls-on-1st-lock-and-ball-2

Turned out to be a sloppy feeder.

I just want to add something to the big pinside pool of knowledge:
I had this exact same problem. intermittant and annoying. but only when one ball was locked.
i started to change switches one by one. after i changed the ball through 1 switch, the problem occured every time i had one ball locked.

It turned out to be a poorly grounded machine and an unwanted connection.
Every time ball lock 1 was activated AND the wire on ball through 1 touched the ball shooter. it would serve another ball.

a bit of bending of the wire solved the problem for good.

switch (resized).jpg