Nagai, Masayoshi, Nobutaka Endo, and Kumada Takatsune. 2007. "Measuring Brain Activities Related to Understanding Using near-Infrared Spectroscopy (Nirs)." In Human Interface and the Management of Information. Methods, Techniques and Tools in Information Design, 884-93. Heidelberg: Springer Berlin
Looks like I was beat to the punch... I've found a study from last year that analyzes the activity in the brain while reading comics. However, it doesn't say much.
The authors use near-infrared spectroscopy to measure blood flow in the brain while reading comics. This technique uses infrared light to measure where blood flows in the brain, which can thus indicate the brain regions involved in various behaviors. They find that "the left prefrontal lobe region is activated when people actively try to understand the comic stories and to memorize their contents for reporting in the future."
However, there are extensive problems with this study. First, the number of stimuli they use is extremely small (only 6 strips) as is their population (13 people... which does not add up to counterbalancing). Comparatively, the study I'm planning will use 180 stimuli per trial (720 strips total) and use somewhere from 24 to 36 people.
Additionally, the increase in blood flow that they observe only occurs in "reported" conditions — where subjects are actively making a judgement about the stimuli, as opposed to scenarios when they are not. This seems more to reflect the well-reported cognitive activation for making judgements than anything about the structure of the comics themselves.
So... this really doesn't tell us much about comics and the brain, but its nice to see other people are at least taking stabs at it as well.