Currently have all of the released Pathfinder data packages and updates for these.
My Human Barbarian 6 [Invulnerable Rager]/Rogue 4 [Scout] normally has a Will save of +5 (modified to +6 with a Cloak of Resistance +1 and conditionally via the Fortified Drinker trait to +8). According to the description of the Rage class feature, he should get a +2 morale bonus to Will saves while raging, but this is not reflected when I click the 'Raging' checkbox on the 'Activated Abilities' section of the 'In-Play' tab. I removed all elements that modified his Will save (Cloak, Fortified Drinker trait) to see if this was a bonus stacking issue, but still end up with an unmodified Will save when Raging.
If I advance him to Barbarian 11 (when he would gain the Greater Rage class feature and a +3 to Will saves while raging) the Will save is still unmodified by the Raging condition, so it appears the problem exists at this level as well.
Edit - Also, poking around in the editor while trying to find the Raging tag, I noticed the following: the hPFRage object under Trackers has an incorrect description, listing the Rage bonuses as +2 Str / Con, +1 Will saves, -2 AC (should be +4 Str / Con, +2 Will Saves, -2 AC).
Edit 2 - Fortified Drinker doesn't modify his Will save in HeroLab, as it is conditional and limited - but I removed it just in case.