Its not you, its MSN. I am in the same boat. 40,000 + pages indexed in Google, 200 pages indexed in MSN. I am not too concerned, and the word is they will be tweaking things this summer so hopefully they will get things right.
We're in the same boat: 64,000 pages indexed on Google, 108,000 on Yahoo, and only 1,400 on MSN.
It doesn't appear to be a crawling issue -- MSNBot has crawled 8,000 URLs in the last 36 hours -- but only our top-level pages and those with inbound links from other sites seem to be showing up in the MSN SERPs.