As I read the rules, a rogue gets the sneak attack bonus if flanking the target, or if the target does not get his dex bonus against the rogue's attack. This means that if the rogue has multiple attacks, and is attacking a flanked or flat-footed target, they will get the sneak attack bonus on all his attacks, as the condition granting the bonus will not change during the attack sequence. However, if an invisble rogue sneaks up to someone already in combat (i.e. not flat-footed), then the target is only denied its dex bonus on the first attack, so only the first attack is a sneak attack (unless some other factor also grants a sneak attack).
Of course not allowing the target to gain dex bonus in the middle of the rogue's attack sequence doesn't seem to break anything.