"Bosses have inherent resistance that can't be broken which comes from level difference (iirc it's 8 points per level, so 24 for targets marked as "Boss"). Such a low score will never give you a 100% resist, but it will reduce your damage a little bit and there's nothing you can do. A boss might have some extra resist to one school or another, but CoE usually takes care of that. You should never need spell penetration in PvE (unless you wanna fight Rage Winterchill as frost for some reason... well, it would help as fire against Supremus but honestly who cares about meters on that fight).
Note that in TBC spells that miss are still displayed as "Resisted" instead of "Missed" because Blizzard is very smart. So you might be getting confusing feedback from your combat text. Just get hitcapped."