I don't use the except on with my blog. My archives etc. aren't showing the whole post, but do show 2-3 paragraphs of it normally. Enough for google to flag it as duplicate I would expect.
A little on my experience also, just for your info. My site at the time had about 210 unique pages. but google webmaster tools had been reporting about 140 indexed pages since passing that point.
After no indexing my category archives this number climbed up to 160 over the next week or so, but again stopped there.
After noindexing my main subpages also, over the last 4 days a few more pages have been added according to google webpages. this would suggest to me its regarding the 3 sources ( post, category, home subpages ) as duplicate content no?
My blog shows 5 articles per page, seems to me its indexing 1 archive or sub page instead of the posts themselves.
I'll post back again in a week or so and let you know if webmaster tools reports more pages indexed now that i've noindexed subpages and category if you like, just for your future reference.
My blog is http://www.andrewkeir.com by the way, probably should have included that earlier :P