EndNote and 2010
This turns out to be this known issue with EndNote - http://www.endnote.com/support/Faqs/Import/faq20.asp
We have EndNote X1. I have just checked the batch of records in question and discover that for 2009, the publication year is indeed present.
The EndNote FAQs give details of how to globally change a batch of records. You could, of course, also edit individual ones.