If all the types of peppers you're growing aren't doing well, that would suggest an environmental problem, and most likely the sitting in water business. It might be better to pot up the pepper plants into ordinary pots and water them when the surface of the soil is dry to the touch, but not so dry its shrunken from the sides of the pot - water thoroughly, and empty out any water in an outer tray or pot 30 minutes later.
As for your snack peppers, they do not always come true from seed anyway - depends whether the original plant was an F1 or other hybrid, which snack peppers likely are, and what pollinated the flowers on those plants you had last year - F1 hybrids are pure bred, and pollinated under controlled conditions, which guarantees the right variety in theany seed produced, if it produces fertile seeds at all (some F1 plants don't).