When I did my first all grain batch (a porter), it didn't occur to me that you put your specialty malts in your mash tun instead of steeping them in a grain bag pre-boil. That beer didn't turn out well and the color was way off (i.e. more red than black). Unless you're making the same bone-headed mistake I did, I'm not really sure what the problem is.
Oh, wait... Large amounts of dark malts lower your mash pH. So it's possible that your mash pH is throwing your efficiency off. Since you're a chemist too, I'm sure you could devise an experiment to see if this is a factor.
EDIT: On a possibly related note, I just did a porter which had lower efficiency than I was expecting (71% versus my 80% running mean). But I think this might be the result of brewing at a substantially higher gravity (1.074 versus 1.050) than normal.