I understood the first time and believe it is a fair call, although it only really matters in the lower levels (where it makes a significant difference!)
Eg. a 5th level wizard casts 3 magic missiles at a target.
A 6th level wizard 5/ Shadow Adept 1 casts 1 magic missile (regular) at a target (CL 6 -4 evocation CL penalty = CL 2)
A 7th level wizard 5/ Shadow Adept 2 using Shadow Conjuration: Magic Missle as a 4th level slot ought to cast 6 shadow magic missiles at the target (CL 7 +4 illusion CL bonus = CL 11)
But because of the glitch outlined for us by Tenebrosity, they would instead cast 2 (CL 7 -4 evocation penalty = CL 3)
Said mage would also get penalised for Shadow Conjuration: Mage Armour, lasting 15 mins (3 game hours) instead of 55 mins (11 game hours).
This is a fair and reasonable change, if possible.
Tenebrosity: Do these penalties also apply to
Greater Shadow Conjuration (Melf's Acid Arrow, Minor Globe of Invunerability) and Shades (Summon Creature VIII or Delayed Blast Fireball)?
[Edit]:
Tenebrosity wrote:Greater Shadow Conjuration suffers the same fate with its version of Melf's Acid Arrow, Web, and Lesser Globe of Invulnerability.