Timing question
 

I ran into a interesting thing I created pair of magic boots and when I put an enhancement bonus for stealth the stealth skill disappeared from the skills and feats tab but reappeared when I I went into the skills tab and added ranks the value reappeared.

here is the script I used

Pre levels 10000
doneif (field[gIsEquip].value = 0)
#enhancementbonus[hero.child[skStealth], 10]

should I have used Pre attributes?

When I changed the same script for another Item and changed the timing from 10000 to 5000 the isssue with the disappearing skill in the skills and feats tab went away why did this happen?

Try:

#enhancementbonus[skStealth, 10]

You want this occurring AFTER other things are calculated, so no don't make it Pre-Attributes. Look at an item in the editor that adds a Stealth bonus and use the same scripts and timing. (Like a Cloak of Elvenkind)