They’re Frightened When They Make the Save
As I've more deeply gone into with this answer, each effect here happens at the same time. There's no mention in the rules about ordering these effects, so they all happen at the final step of resolving the check for the attack.
Pathfinder has many types of checks, from skill checks to attack rolls to saving throws, but they all follow these basic steps.
- Roll a d20 and identify the modifiers, bonuses, and penalties that apply.
- Calculate the result.
- Compare the result to the difficulty class (DC).
- Determine the degree of success and the effect.
In this case when you critically hit with your fearsome frost weapon using Flurry of Blows and with something that gives you the brawling critical specialization effect, the effect is:
- You hit and deal double damage (described under the rules for damage)
In the midst of combat, you attempt checks to determine if you can damage your foe with weapons, spells, or alchemical concoctions. On a successful check, you hit and deal damage.
- The target becomes frightened 1
- The target is slowed 1 until the end of your next turn unless it succeeds at a DC 24 Fortitude save.
- The target must succeed at a Fortitude save against your class DC or be stunned 1 (or stunned 3 on a critical failure)
- The target must succeed at a Fortitude save against your class DC or be slowed 1 until the end of your next turn.
As each of these effects happen at the same time, the creature is frightened when they are hit by the weapon and that penalty would apply to each of the simultaneously applied saves. The saves aren't made before or after the attack hits, but are rather made exactly when the attack hits and the creature becomes frightened.
Where Things Would be Different
Of note, this would be substantially different if the fearsome rune's effect gave a save to resist it.
As described above in the steps for handling checks, the effect of making that saving throw check would happen after rolling a d20 and identifying modifiers to the roll. With each rune's save happening at the same time this means the resulting effect(s) would happen after making those other checks—that they would only be frightened after having made those saves.