Here's one I can't figure out...

My bike's drivetrain was set up in its current format roughly 8 months ago, and is as follows:

Surly Basic/Junior hub, 16t Dura Ace 3/32 cog (2 years' use)
Suntour Superbe double crank with 45t Sugino ring (2 years' use)
Campagnolo AC-H bottom brack (8 months' use)
SRAM PC-48 3/32 chain (1 month's use)

The Campy bottom bracket was installed 8 months ago to replace a shot Superbe track bottom bracket, and the chainline was pretty good when it was done (by my LBS). A millimeter or two off, but not so much that it made noise. I rode this setup in Chicago for a solid six months, no noise, with the same SRAM chain for five of those months.

Last month, when I replaced the chain, I noticed that a 'click' had developed in my drivetrain. This progressively got worse over time, and now there are pronounced clicks throughout my pedal stroke.

I went over all the usual culprits: cleaned/lubed the chain, regreased/reinstalled the chainring bolts, checked the bottom bracket (spins smooth), cleaned/reinstalled the crank... all to no avail. I even went as far as to put the old chain back on it, but it still made the same clicking sounds.

My LBS (Biowheels in Cincinnati) diagnosed the problem as poor chainline. Indeed, the chainline is still off by a couple of millimeters, but why does it matter all of a sudden? How is it that for five months this difference didn't make any noise, and now it has rapidly degraded into a clicking drivetrain?

Any insight is appreciated.