The DR from the feat doesn't stack but is in addition

The feat Roll with It (Savage Species 39) says

Benefit: You gain damage reduction 2/—. This applies in addition to any damage reduction you have from other sources. Damage reduction cannot reduce damage you take to less than 0.
Special: You may take this feat multiple times.

Thus the damage reduction from each iteration of the feat is in addition to any other damage reduction the creature already possesses. Don't think of it as stacking (i.e. combining for a cumulative effect and not generally possible with damage reduction); instead, think of it as another layer of damage reduction (also usually not possible, but the feat's specific phrasing trumps the general rules for DR).

In other words, after damage has been dealt to the creature and the creature's other damage reduction has reduced damage appropriately, then the creature applies the damage reduction from the feat Roll with It, each iteration of the feat applying individually and sequentially.

For example, a dwarf barbarian 7 with the feat Roll with It that would have been dealt 10 points of damage by a longsword applies his barbarian level's DR 1/— to that damage first then the DR 2/— from the feat Roll with It. The dwarf is dealt 7 points of damage. Were the dwarf to have taken the feat Roll with It twice, he would apply his barbarian DR 1/— then his first Roll with It DR 2/— then his second Roll with It DR 2/— so that the longsword would deal 5 points of damage.

The feat's phrasing is unique, and it (rather pointlessly, in my opinion) breaks some rules, but feats are allowed to do that, so it's no big deal. It would have been much clearer were the feat's Benefit simply to have read that it reduced the damage from manufactured and natural weapons by 2 each time the feat's picked, but that's not what we got.

If you still don't like it, have the DM fix it

The DM is allowed to revise to 3.5 standards items from Dungeons and Dragons, Third Edition that weren't upgraded to 3.5. The Dungeon Master's Guide (2003) says

This [i.e. from Dungeons and Dragons, Third Edition to Dungeons and Dragons 3.5] is an upgrade of the d20 System, not a new edition of the game. This revision is compatible with existing products, and these products can be used with the revision with only minor adjustments. (4)

The DM, presumably, makes these minor adjustments. This, for your group, may be one.

Yes

The spell monstrous physique iii allows you to polymorph into a monstrous humanoid, which is minotaur's type. Natural Cunning is listed as one of the abilities you can gain from this spell, if the base form has it, and the minotaur does:

Natural Cunning (Ex) Although minotaurs are not especially intelligent, they possess innate cunning and logical ability. This gives them immunity to maze spells and prevents them from ever becoming lost. Further, they are never caught flat-footed.

Since maze is a spell with a duration, you can't be affected by it if you are a minotaur, since while in minotaur form you cannot be affected by the maze spell or lost in a maze.

According to the rules on immunity, a creature immune to a spell "does not suffer from its effects", which means that even if it began under a spell's effect, it would not suffer the spell's effects once it gained immunity.

A creature with immunities takes no damage from listed sources. Immunities can also apply to afflictions, conditions, spells (based on school, level, or save type), and other effects. A creature that is immune does not suffer from these effects, or any secondary effects that are triggered due to an immune effect.

This specifically refers to the Immunity special quality, but I think it's reasonable to assume that the ability Natural Cunning, which grants "immunity to maze spells", works the same as an ability called Immunity: maze.