The headband of vast intelligence (the most common example) gives skill points equal to HD of the creature donning it into a fixed skill chosen when the item is created. This is exactly to avoid this problem, and also to avoid the possibility to reassigning the points just by removing the item and donning it again for 24 hours. It's a special ruling because it's an easily lost and regained bonus. It' safest and easiest to extend this ruling to every other permanent bonus to int from items.
If the int bonus is given by actual changes of the ability score (like level advancements, wishes and tomes) you get retroactive skill points as stated in the ability score section.