Ultimately, the DM should use whichever version he likes best - since any and all effects are limited to his game, he gets the call.
However, in general my recommendation would be to use the most recent version, with any errata that were published for that book applied. Which, in the case of nature's favour means the version from the "Spell Compendium", I think.
Yeah, that takes it back up to +5 max and makes it a swift action.
I just compare it to divine favor, and figured they would be the same spell, just one for regular weapons the other for natural weapons.
Note that it's also a 2nd level spell, where divine favor is 1st level. That probably explains the difference in the maximum allowed bonus. (Well, that and also that it only affects animals.)
Incidentally, it is my opinion that virtually any spell that has a casting time of a Swift or Immediate action is questionable at best - that's the equivalent of having the Quicken Spell feat applied, which means that the other effects should be roughly equivalent to a spell four levels lower (which is never the case). But that's just my opinion, and not really related to RAW in any way.![]()

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.