What fountain pens are you using? After a couple years of using Platinum Carbon Black ink (waterproof, lightfast, pigmented) in many different fountain pens, I have not had this problem, except for some Jinhao fude nib I left for several months with a bad cap. For the moment I mostly use it with Platinum pens, but I've had it in other pens also. The Platinum pens have a good cap and some of them have a feed adjusted for the Platinum Carbon black ink. And they cost from very cheap to very expensive ;) There are more brands who make waterproof and lightfast fountain pen inks which I have less experience with (Sailor, Pelikan, Rohrer & Klingner I think all have special line inks for this). One have to be more careful and clean the pens more often then if used a regular fountain pen ink. And I would not put it in a vintage pen with a sac filler, perhaps. But in general I've had no problem with clogging, so it makes me curious why it is clogging your pens :) In my experience some of my Jinhao pens is very prone to drying out in the nib.

I recently discovered a video where they actually put the zebra G nib on a funtain pen, which is the best of 2 worlds (I have 2 here at home and you can make your own if you are a bit crafty). Sadly the custom funtain pen, while it's the best by far for inking, isn't very found of the carbon ink I use and force me to clean more than I would like to. I'm investigating for other inks that would be more compatible because it's a really good and portative setup. Except for the G nib custom funtain pen, I use a jinhao 301 funtain pen which does support the carbon ink without issue and a pilot V5 techpoint (the one with metal nib). Hope that help :)

My experience is that some fountain pens just doesn't like certain inks, or ink brands regardless of if they are pigmented waterproof or not. If you like waterproof inks, have you tried a different brand? There aren't that many to choose from, but as Elvis Murray wrote, Jetpens have a good guide about waterproof inks. Personally I have tried Platinum Carbon Ink and DeAtramentis Document Ink. The Platinum clogs after a couple of weeks in the pen, the DeAtramentis does not.

Are you using waterproof ink for your fountain pens? There are many fountain pens that really do not like waterproof/archival ink. But there are also fountain pens out there that have archival ink especially formulated for the pen. i would look into those if possible. I use Pigma Micron PN's but i'm really interested in getting into Fountain Pens for drawing soon. Jetpens i believe has a good guide for ink and fountain pens and i think they have a section on archival quality. hope that helps.