Well, yeah, effects ending after time start ticking when they're applied.
One way to solve this is to split it into 2 separate effects - one that's applied by attacks and one that handles the actual stunning.
1) Stun applied by abilities/etc.
End after Start Turn and applies the 2nd stun effect via the End Status Effect Casts. Doesn't do anything else (e.g. blocking actions, etc.).
2) Time-based stun.
Ends after Time, blocks actions, etc.
That should do the trick, though I haven't tested it.