[dungeonguru]

It likely has to deal with timing, would have to see all the scripts being applied on the hero to be sure.

Have you looked at the UA article Feats for Skills code? The feat Acrobat has some code in there that does exactly what you want for Acrobatics, but doesn't leave a second copy on the sheet. Should be easily modified for whatever skill you want.

The code runs Post-Level at 15500, which is after Helper.Proficient tags are assigned on most abilities (around 10000) but before the proficiency & double proficiency tags are pushed (around 16000 if I remember).

doneif (tagis[Helper.ShowSpec] = 0)
doneif (tagis[Helper.Disable] <> 0)

foreach pick in hero from BaseSkill where "thingid.skAcrobat"
     if (eachpick.tagis[Helper.Proficient] = 0) then 
          perform eachpick.assign[Helper.Proficient]
     elseif (eachpick.tagis[Helper.Proficient] <> 0) then
          perform eachpick.assign[Helper.ProfDouble]
     endif
nexteach