Just shooting from the hip here, but the text box (as with most text boxes in page layout programs) appears to presume that you want the type aligned with the top of the box, and so it automatically shifts the type upward. The Text Tool makes no such presumption.

Looks like Nick is right. I just tried it with a layered font I'm working on - top is text box, bottom text tool:

I like your thinking oldnick.

But after testing two different multi layered fonts, Detroit and Frontage using the text box in illustrator, I've found that they both behave differently.

Detroit automatically shifts the layers around like in daverowland's example.

However, Frontage somehow always sticks to the baseline, with the shadows dropping into the descender line. This creates the perfect vertical alignment, so you can type anything in the box and duplicate the box to change the type into say the shadow style.

I'll keep trying some possible solutions, I thought it might be a simple checkbox on export to retain the glyph ruler/metric settings.

Interesting. Has anyone isolated this issue yet?

It might help to standardize the BBox vertical metrics. Some cheating may be necessary.

http://typophile.com/node/98477

If it's any help, I tried just about every combination of metrics I could think of and couldn't get round the problem. Don't suppose that is any help!!