When I created my character, I set perception to 6 and took the Four Eyes perk. The perk seems to be working correctly, meaning I have 5 perception when not wearing glasses and 7 perception when I am. Unfortunately, the level up menu will not allow me to take any perks that require 6 perception. Even if I pick the Intense Training perk, it shows perception as being 5. It was my understanding that the level up menu did not take into account things that add or subtract from your S.P.E.C.I.A.L. attributes, like clothing, food and whatnot.

Has anyone else noticed this?

This happens because the perk works by reducing your base Perception by 1 and then adding +2 perception to all glasses. The level up menu does not take into account an equipment or consumables, but it is affected by perks that increase (or in this case decrease) your base stats or skills.

Not really a bug...just a clunky game mechanic.

Just because you don't like it doesn't mean it's "clunky". There is nothing clunky about it. It's just how it is.

Companion control? That's clunky.
Animations? That's clunky.
Having to add .dll files just to make the game playable around humans? That's clunky.

There is nothing clunky about this.

It's clunky because the way the perk is described in it's description doesn't match up with the way it actually works. It says you lose 1 perception when you're not wearing glasses and gain 1 when you do, which implies that your base perception is unaffected. What actually happens, and what the description should say is that you lose 1 perception permanently and gain 2 when wearing glasses.

There is a mod to fix this. http://www.newvegasnexus.com/downloads/file.php?id=35652

Yeah exactly. This is how it should be, and how it is describe by the tooltip in game. Without the mod....it's clunky.