Stop quarelling girls, you're both pretty!
Umbran is right: both F&P and D&Dg contain optional rules. You don't need them to play D&D properly, and you don't need them to play F&P properly. So if elminster is indeed immune to time stop (which would maybe mean that he could not be "cheated of 1d4 rounds", because he wouldn't choose an immunity that would not help him at all), that means that Mystra makes it so. There are no core rules that state how gods behave - and if I recall properly, the DMG states that they are far more powerful than any mortal and can more or less do what they want. And allowing someone to have no ill effects of a certain 9th-level spell is nothing compared to things like creating own demiplanes or whole races. They don't have to follow the spellcasting rules, at least not when considering only core rules.
On the other hand, though, you must consider that WotC doesn't intend to make their "official gods" behave as they want - especially if they just released 2 books on how gods behave and what stats they have. The write-ups of characters in the Rulebooks are considered to follow all the published material about the Realms. The Forgotten Realms, as they are presented in the rule books, have a canon storyline. This storyline doesn't contain an all-mighty entity called "Dungeon Master" as the hightest instance. It contains a bunch of gods and an Overpower (Lord Ao), who maintains the balance (and he himself reports to a higher entity, but within the Realmsspace he is all-mighty). Ao wouldn't want Mystra to mess about with the laws of the cosmology, doing whatever she wants. Especially not making senseless rules. So Mystra (and all the other gods) have to obay the rules from F&P (and probably D&Dg, too)
Now, being immune to Time Stop can only be nonsense: Either you are immune to its effects, meaning you cannot profit from it, not cast it, or another spellcaster cannot gain benefits from it against you. Which is nonsense, too, as the spell speeds up it's caster, and does nothing to the enemies who seem frozen.
So, Elminster is clearly not meant to be immune to Time Stop. As some errata chaged that into Temporal Stasis, it's fine