I probably shouldn't have used the word "clog".
What actually happens is that dust builds up in the hidden corners of the slot that the gate slides in. Even when hanging vertically, but not nearly as often as when they were horizontal. Once the dust builds up in the corners, the gate will not fully close.
What I think may be happening is that dust settles on the track and then the gate pushes it up into the corners when you close it. Eventually the gate doesn't fully seal. I can tell not just by the air flow, but also by the dull thud when closing the gates vs. the solid click when clean.
I bought 2 "self-cleaning" gates from Lee Valley but they leak too much for me. They have an open slot so that the gate pushes the dust out, but the slot also acts as a hole in the system. Dumb.
Full disclosure: These are 2 1/2" plastic gates from Woodcraft. I need to look for some 2 1/2" metal gates of the non-self cleaning style. Maybe the thinner metal gate won't push as much dust into the corners.