Probably time to start tracing the shooter lane feeder circuit back to the Aux Power Board and to the MPU. It might reveal a flaky transistor. Is the spinner flasher working as expected? The ball feeder is on the A-side of that circuit while the spinner is on the C-side.

Any luck? Here's something to read about troubleshooting switches that might give you some ideas:

http://techniek.flipperwinkel.nl/wms11/index3.htm#switch

Not sure if it is related but does it behave the same with 2, 3 or 4 players?

Also, if the switch matrix is confused due to a flaky switch then it's going to be a completely unrelated switch. If switch 22 (left lock lower - col 3, row 6) is the one that starts the chain of events then switch 43 (col 6, row 3) and switch 19 (col 3, row 3) need to be checked. The fourth switch to make the "square" is 46 (col 6, row 6) but it is not used in Whirlwind.

If not a switch (or simply a bad wire) then it's most likely on the MPU.