First, I'll direct you here: FFXIclopedia's entry on Shields
Specifically, I'll quote two paragraphs from there:
The smaller shields will block more frequently, but will reduce the damage by a small amount whereas the larger shield will block more damage but will trigger less often.
Size 3 shields generally offer the most efficient balance of block rate and damage reduction outside of the Aegis. A Paladin with enough Shield Skill can get close to the block rate cap with a size 3 shield, but not with a size 4.
I know that doesn't constitute unrefutable proof, but it doesn't take long to test it out yourself. Master Shield isn't that expensive. And, you should have received a Kite Shield, at least, when you unlocked PLD. If not, it's fairly cheap to get a good size 3 shield you can use. Go out, find some EM mobs, and go to town blocking them. You can eyeball the difference on this, really. Yeah, the Master Shield will block more often than the others due to higher shield gear, as well, so you could always grab a different buckler if you think it's the +shield skill gear affecting it, but the results end up the same.
There were a ton of posts about this shortly after the change occurred, but they're buried pretty far back. If you're looking for more information, you could go digging back through a few years worth of posts.
Edit: Here's a specific link I came across trying to find things to link for you. http://ffxi.allakhazam.com/db/jobs.html?fjob=5&mid=1180062662109938677 Edited, Apr 8th 2009 1:32pm by Dracoth
Leviathan - PLD90, BLU90, MNK 90, DRG 78