Test the trough switches one at a time in switch test.

Empty the trough.
Add one ball to the trough. The switches should trigger: left, center, right.
Add another ball to the trough. The switches should trigger: left, center.
Add another ball to the trough. The switch should trigger: left

I would think possibly your center switch is sometimes stuck open.

I'd suspect the trough switches. Particularly the center one. Although if that was the case, locking the first ball in multiball would sometimes act weird, too.

A stuck switch on the playfield could possibly make the game think there's already a ball in play at the beginning of Whirlpool multiball...

I was also going to suggest testing the switches in no way out in switch test mode, but you'll probably find that they're all OK, especially since you mentioned fixing them.

Is the shooter lane switch working properly?

I doubt it's related, but where's 68-disaster drop enter. That's the opto on the right ramp entrance? I think that's the only opto you're missing. If that one is intermittent, it could be mistaken for a ball in play.

Isn't that backwards, though?

Haha. The next thing I would have told you is that that opto is really easy to get to from underneath, but you figured that out.

It's definitely too early to call it fixed, but it could be. I had a blown opto there and everything actually still works 100% normally (but with a credit dot). If you didn't have a credit dot, that would probably mean that the opto is triggered intermittently. If it flickered on and off while your whirlpool multiball was trying to start, I think that's a reasonable explanation as to why the game might not serve a ball, as it thinks there's already one on the playfield.

Happy to help! I just got my Whitewater about six months ago. Installed a new playfield, all new ramps, and new boulders, so I learned a LOT in the process of doing all that.

Also... best game ever.