Sterilize jars and lids. I put them in the dishwasher and pull them out when still hot to use. You can also put Put empty jars on a rack in a boiling-water canner or a deep 8- to 10-quart pot. Keep jars and lids submerged in hot water (not boiling), covered, until ready to use.
Pulse bell peppers with red-pepper flakes in a food processor until finely chopped. Mixture will measure about 2 1/2 cups after being chopped.
Mix together pectin and 1/4 cup sugar in a small bowl.
Stir together pepper mixture, vinegar, butter, salt, and remaining 3 cups sugar in a 5- to 6-quart heavy pot. Bring to a boil over high heat, then continue to boil vigorously, stirring occasionally, 5 minutes. Gradually add pectin mixture, whisking constantly. Return jelly to a boil, stirring constantly, and boil, stirring constantly, 1 to 2 minutes, mixture will thicken slightly. Remove from heat.
Carefully remove jars and lids with canning tongs, drain jars upside down on a clean kitchen towel and quickly dry lids. Invert jars and immediately ladle hot jelly into jars, leaving 1/4 inch of space at the top. I keep a small jelly jar on hand in case I don't have enough to fill the 5th half-pint jar. If needed, run a skewer or plastic spatula between jelly and sides of jars to eliminate any air bubbles. Wipe off rims of filled jars with a damp towel, then screw on lids.
Put sealed jars on rack in canner or pot and add enough hot water to cover lids by at least 1 inch. Do not process the partially full jar if you had one. Cover it with a lid and keep in the refrigerator. Bring water to a full boil then boil jelly, covered, 15 minutes. Use canning tongs to carefully transfer jars with canning tongs onto a towel to cool and seal. When you hear a ping, that means that the jar has sealed. Jelly will thicken as it cools. After jars have cooled, 12 to 24 hours, check center of each lid to see that it's concave. Put any jars that haven't sealed properly in the refrigerator and use them first along with jar that was only partially full.