If its a Toyota Dagupan unit then it is quite likely that the driver runs Kennon several times a day since Baguio - Dagupan is a busy commuter route. I normally take Kennon Rd. as i enjoy the scenery and sweeping curves a lot as the banking is done well... plus its faster. I only avoid Kennon if its been raining hard (as rocks sometimes fall on the road).
The air filter should be cleaned everytime you go in for service and then replaced every 5,000kms. Diesels are quite sensitive to clogged air filters as compared to gas units. Another filter i replace every 20,000kms is the fuel filter element; although the owners manual doesnt call for it, the original element (not the fuel filter assembly) is pretty cheap at the CASA so i just change it since its a practice that i do with all our cars before.
Now that the topic on the foul smelling AC was brought up, i do recall that my wife was complaining about a palengke smell when i start up the AC on some mornings in our Altis.

I thought it was mainly because of the trapo i used to wipe the interior at times.