tested with 1.6.10, where i found the bug, then with 1.6.12 after i saw that there was an update, while i was writing the bug report.

i've found this bug only with thaumium fortress armor for now:
-1.6.10
when i look at the armor value when the armor is in the inventory it shows what i think is the intended value, +12 locational armor thoughness/+19 locational armor for the helm for example. When i equip the armor it shows +3 armor thoughness/+3 armor and on the bottom +7 locational armor.
totally not a visual bug as i get double the damage (tested with primitive mob's skeleton warrior with a sword)

-1.6.12
now the armor show always +3 armor thoughness/+3 armor and +7 locational armor but it looks like it is a visual bug as it look's like i'm getting the same damage with diamond armor

Thaumcraft is closed-source, which makes tracking this down pretty much impossible. Sorry.