(M&M 3e) Flaw counting as extra for point calculation?

[maniacalsounds]

Is this a bug in the software, or am I missing something?

I have a player with a Cumulative Affliction 9, Permanent, Affects Corporeal.

So affliction is 1pp/rank => 9pp.
Cumulative is 1pp/rank => 9pp.
Permanent is -1pp/rank, but also need increased duration at 1pp/rank => 0pp (net)
Affects Corporeal is 1pp/rank => 9pp.

So I get that the cost should be 27pp. But Hero Lab shows 45pp!

At the top they say (1/r +3ex) x 9r = 45pp. The 1/r is right, since affliction is 1pp/rank. The 9r is right since it's rank 9. But it looks like it's counting cumulative, permanent, and increased duration as 3 extras, whereas one of them is actually a flaw that should reduce cost!

Is this a bug, or am I missing something? How would you suggest I navigate around this and make up for these points in HL? Thanks!