Do you have thick plants in the tank? I can't imagine other fish could eat a pleco if it wanted to... Maybe they're just hidden somewhere and slowly rotting?
If it was me, I'd take all the large decor out (including plants) and see if you find a couple half-decomposed pleco corpses.
You mentioned that according to the strips everything is "normal". What exactly did the strips say?
Many guides for the strips say that ammonia should be <3 and nitrite should be <5, but really they should be 0.\
Also, check the PH. It could be extremely low or extremely high, which would cause similiar symptoms to poisoning. Usually "poisoning" can be temporarily treated by doing frequent water changes with fresh dechlorinated water. (w/cs will remove nitrogen compounds, other "poisons" from the air or cleaning supplies, and will slowly bring the PH closer to that of your tap water- unfortnately will also remove meds and salt.)
I also agree that you should use a magnifier and look at these "holes" you speak of closely and tell us what they look like. Are they holes? Do you mean gills when you say holes? Are they inflamed (red)? Do they have a "fuzziness" (mold/fungus) around them?
I've had sick fish like you're describing before, but usually they didn't live 24hrs after I noticed the symptoms...
definately need to take out the carbon if you're using meds, but you probably already knew that.
Worst case scenario (everything dies), scrub the tank with either strong salt water (and rinse thoroughly) or mild bleach solution (rinse thoroughly and then rinse with water again with a triple does of dechlorinator- dechlorinator neutralises bleach since it's basically chlorine gas dissolved in inert liquid) and start up again with just swordtails.
They're MUCH easier to keep, and stay small.