tested on 6.07.01.
as title says Wings of Flying are missing +5 Flying competence bonus like stated
https://www.d20pfsrd.com/magic-items/wondrous-items/r-z/wings-of-flying/
win 7 x64
The bonus is only applicable if the wearer speaks the command word. Otherwise it is just a cloak. Hence bonus is not permanent and no misc modifier.
I would propose that the bonus should be displayed as a conditional modifier if wings of flying are equipped.
I tested with v 6. 08.00 RC2, pleasefind screenshots and .pcg file attached
the thing is, u only can skill in fly if u have the ability to acutal fly. that means, if u dont wear the wings u cannot even use the skill fly. (maybe only in the rare occurance of magical flight)
Wings of Flying offer a Temporary Bonus when activated. After equipping them, look under Temporary Bonuses for Items. Click on wings of flying and the bonus will be added.