Well, I'm officially going back to using salt. I never had these kinds of problems when I used to use salt all the time, but I stopped because everyone said it was bad for plants. Then I got ich, twice, for the first time ever, had fish that were flashing, had some weird unexplainable deaths, and now this. So salt is now returning.
I've got the remaining cory in a hospital tank with malachite green, formalin, and jungle fungus clear. He's not acting funny yet but his finnage doesn't look so good. I've also increased the temp on the main tank to try to kill any parasites or what have you that could be causing the issues along with the salt.