If anyone stumbles on this random post when looking for duplicate Google Reader post solutions, I think I may have discovered the root cause of the issue, and it's annoying.
The blog had many many atom feeds, but only one primary. The primary feed listed the 25 most recent posts at any given time, but beyond that feed, there were other discoverable feeds listed in the meta data of the content. These included category feeds, comment feeds, page specific feeds, popular posts feeds, etc. It seems that Google Reader, in all of its wisdom, was crawling all of these feeds and treating them all as absolutely distinct feeds and items, even though they all had the same unique id for the posts (url for the post). Once I removed all of these as discoverable feeds, and also made sure to redirect the main non www feed to the one with www, to ensure all urls are unique and not duplicated, all seems to be well with the world and google reader is no longer duplicating the content.
Well, that was many months of annoying and frustrating items trying to troubleshoot a service that has absolutely not ability to debug or provide useful information for a developer.
I hope this helps someone...someday.
