BONUS:SKILLRANK only applies Manually granted over VIRTUAL and AUTO nature granted.

FROM

ABILITY of any form
MULT:YES
Must have a BONUS that references the choice, e.g.:
BONUS:SKILLRANK|%LIST|1

Grant the Ability as Virtual:
VFEAT:MyAbility(Some Choice)

Then take it as normal with a different choice.

Make sure all of the appropriate skill ranks are correct