This really is a loaded question. Percentages are very complex. It's been a long time since I've worried about this stuff.
As screwup said, percentages are based off of your base stats (though some buffs and added effects are included, it depends on what the buff does).
Base stats are additive and the percentage boosts to those stats are additive. But then there are the stats based on base stats, such as attack, heal, evasion, defense. These stats are affected in several ways including being derived from your base stats (power/stam give 1.2 p.def, agility gives p. eva, int gives magic evasion, etc), they are directly increased as a stat (+2000 physical def), sometimes they are a percentage stat that is increased as stat (might say plus 25% evasion and give you 250 evasion stat for a direct 25% increase), they can be increased by an actual percentage like that title implies (which base int should add to the base m. eva stat and any actual m. eva stat added in, before adding the percentage bonus to it [which itself is additive with other percentage bonus from that stat]), buffs for direct base stats (and passives) should add in directly before percentages are applied and percentage based buffs should add up with other percentage bonuses when applied. I feel like i'm forgetting something else...
At least that is how I think it all operates.
Anyways, it all intermingles in one huge complex system, which makes it rather difficult to actually calculate what it should be. There is a chance that it is off, but I'd rather hope it is working right and you just don't know your actual base that it is operating off of for the magic evasion stat (it is honestly rather hard to figure out pure base of a derived stat (or any stat for that matter) sometimes, particularly when there is a passive interfering with it).