On your stat window, your Mdef says ###+### correct? I haven't played in a while, but I remember the first number being a percentage reduction given by gear that is calculated first. Say your mdef is 90+whatever; that means your reducing magic damage by 90%. The second number is given by your INT stat (and LUK? I don't remember). Any way, say your MDEF is 90+100. This means that you reduce 90% of damage, then take off 100 from whatever is left. So a JT that is supposed to hit you for 10k damage will hit you for only 900, since 10% of 10k is 1000, then subract 100, which is 900.
Also, cheaper MDEF gear is out there. Don't know your budget or whatever, but there are options if you aren't geared to the teeth.
Crystal Pumps (10 mdef, shoes), Wedding Dress (15 MDEF, body armor), Ragamuffin Manteau (10 MDEF, garment), MANY headgears (10 MDEF), Rosary [ 0 ] (5 MDEF)
Also, I believe 100 mdef is impossible now. I think the max is 95, which is achievable by any class. But honestly, that much is serious overkill, unless you fighting someone with HW of course.
Being able to totally avoid a spell is something else entirely, however. Back when we were Aegis, my ninja could walk around ignoring everything with Cicada, AutoGuard, Improv Def, and 100 MDEF, but many spells would still hit me for 1 damage, while others would miss. Doesn't make sense considering my MDEF should be blacking 100 + whatever, but that's what was happening.