Did you remember that if he makes a ranged attack in the same round as he uses both hands to attack, the ranged attack does not gain the reduction in penalty that the Two-Weapon Fighting feat provides?
Example:
With BAB +10/+5, melee dagger bonus of +1 (say Weapon Focus and Str 10), ranged dagger bonus of +4 (say Weapon Focus and Dex 16), he could :
a/ Make two melee attacks with his right dagger and one with his left at +9/+9/+4 (+10 +1 -2t / +10 +1 -2t / +5 +1 -2t)
t: -4 for attacking with two weapons, reduced to -2 with TWF feat
b/ Throw three daggers with his right hand using Rapid Shot at +12/+12/+7 (+10 +4 -2r / +10 +4 -2r / +5 +4 -2r)
r: -2 for Rapid Shot
c/ Make two melee attacks with his right dagger, and then throw it using Rapid shot at +9/+9/+7 (+10 +1 -2r / +10 +1 -2r / +5 +4 -2r)
r: -2 for Rapid Shot
d/ Throw two daggers with his right hand and one with his left at +10/+10/+5 (+10 +4 -4t / +10 +4 -4t / +5 +4 -4t)
t: -4 for attacking with two weapons, not reduced by TWF
e/ Throw three daggers with his right hand using rapid shot and one with his left hand at +8/+8/+8/+3 (+10 +4 -4t -2r / +10 +4 -4t -2r / +10 +4 -4t -2r / +5 +4 -4t -2r)
r: -2 for Rapid Shot
t: -4 for attacking with two weapons, not reduced by TWF
e/ Make two melee attacks with his right hand, one with his left, and throw his right dagger using rapid shot at +7/+7/+2 and +8 (+10 +1 -2t1 -2r / +10 +1 -2t1 -2r / +5 +1 -2t1 -2r and +10 +4 -4t2 -2r)
r: -2 for Rapid Shot
t1: -4 for attacking with two weapons, reduced to -2 with TWF feat
t2: -4 for attacking with two weapons, not reduced by TWF
... or various other combinations.
-Hyp.