df2x4 - all you're seeing there is a minor failure at the glue layer between the sheets of glass, the windshield is laminated safety glass. I wouldn't look at that as a symptom of anything else and certainly not evidence of a water leak. The windshield is glued on the back side of the edges against the body with a black urethane adhesive, it can fail, and also if the windshield was ever replaced the installer may not have done as good a job as the factory. I'd kinda, maybe, sorta suggest removing the A-pillar trim and have someone try aiming a water hose along the edges of the glass, varying pressure and position, to see if you spot any leakage inside using a bright light. Only reason I'm hesitant to suggest it is that it's easy to break the trim, and it may not net you a positive result anyway. :/
The way the air inlet inside the cowl is designed is that it is simply a raised 4-sided wall in the floor of the cowl area. That's why -most- of the crud that gets in past the cowl plastic doesn't end up inside your airbox, and pretty much all the water stays out (normally); but stuff like dust, small leaves, and pine needles get through and clog up your evaporator core fins. They blow around inside the cowl and make it over the wall. For it to actually leak water into the HVAC air intake the bottom edge of it along the cowl floor would need a rust-through spot.
Richard
Thanks for the info! Well I'm kind of at a loss then... I'll have my mechanic look at it next time it goes in for something and see what he says. I have a feeling it may still be the windshield though. I've heard it make some weird little creaks and groans in super hot weather, and it's the original glass, never been removed.