Run the red and green peppers through a coarse grinder, or pulse in a food processor until finely chopped. Transfer to a strainer, and drain really well. This is key to your success.
While the peppers are draining, sterilize your jars by boiling or using the dishwasher. Keep hot.
In a large pot, combine the peppers, vinegar, white sugar, red pepper flakes and pectin. Bring to a rolling boil over high heat while stirring constantly. A rolling boil is one that does not stop when stirred. Boil for 1 minute.
Remove from the heat, and ladle into hot sterile jars to within 1/2 inch of the top. Seal with new lids and rings. Place into a boiling water bath for 15 minutes. The jars should be completely covered by water. Remove and let cool. The jelly will be somewhat loose. The last jar may not be full. Just refrigerate, and use within a week or two.