I have the same problem with PSP games downloaded via NPSbrowser. PSP games I acquired via other methods transfer fine as well as PSX and Vita games.
Perhaps you are having this problem with PSP games only as well?
I believe it's due to pkg2zip not supporting PSP extraction on version 1.8 properly however that's purely a guess as I came here looking to solve this problem myself.
I'd appreciate any suggestions people have that would lead to a resolution for this.