This has probably been reported before, however:
Trying to sneak attack NPC opponents armed with missile weapons seems to work only about one-tenth to one-sixth the times it is supposed to (in essence, identical situations wherein Sneak Attack works against a melee opponent).
Not sure if it's anything anybody can do anything about, but thought I'd drop it here.
Having played many rogues, I can tell you that if you are close enough to trigger sneak attack, and they are not aiming at you, it will work just fine everytime.
I've never heard about this problem. Is the NPC targeting you? I don't believe you should be getting a sneak attack if they're targeting you with a ranged weapon.
They have to be engaged in combat with another person, in melee, or be otherwise flat-footed/unaware of your presence. It also won't work if they're targeting you, as has been said.
EDIT: You also have to be within 30 ft. of the enemy, which is rather close.
All these conditions were met. Another player also experienced the same issue.
EDIT: I, too, have played several rogues over the years. That is why this surprised me.
Elaboration:
a) The targeted enemies were either flat-footed, unaware of our presence, or targeting different players.
b) Attacks were both done as ordinary melee attacks, ranged attacks within thirty feet, or melee attacks of opportunity.
c) The same enemies were also targeted while they were fleeing, under the same circumstances as above.
Under several circumstances, a sneak attack did indeed occur when attacking under these circumstances - but between 90 and 60% of the times, did not, even when the attack occurred under identic circumstances. Enemies equipped with or using melee weapons/were animals/were monsters could be attacked using Sneak Attacks normally.
Some of the creatures have an npc version of either uncanny dodge or defensive awareness (I forget which) that kind of messes with sneak attacks. Notably some Ogres and Stargazer Flayers :P.
VP: That could very well be the issue! Will have to check it out. Cheers!