aakk9999 - 9:59 am on Jan 9, 2013 (gmt 0)
From your sample URL I would imagine you have had somewhere relative path problem OR redirect problem. Relative path problem can occur if you internally linking to URL where href does not have a full path root / and where your page where the link is on has folders.
It could also be caused by badly implemented site move.
Interesting is that you said that some of these URLs that return 404 have good incoming links - what would indicate that such URLs have existed for some time - long enough to acquire good links.