This is something that I ran into myself and then happened to stumble on the answer on guess where? The Zune site. What you are reporting here is expected behavior, maybe not what you would expect, but it is noted on the Zune forums FAQ. Which I found by just clicking on the plays link on your Zune card page.
From the following link:
http://forums.zune.net/30/ShowPost.aspx
"Playing most songs within your collection will result in a play being uploaded to your recently played list, but there will be some songs that do not. We have worked hard to extend coverage beyond what is currently available in the Zune Marketplace and are committed to expanding the coverage further in the future.
Update: Playcount totals within your profile's most-played artist list only reflect plays recorded within the past 28 days. Note that this will also affect your placement on top listener lists. Top listener lists only take into account plays recorded within the past 28 days."
