I run word 2007 with endnote X3.01 on win7 x64. If I add references to a document, and format them, I am no longer able to do word counts. The wordcount at the bottom left of word becomes greyed out & no longer works - although the legacy shortcut (alt-T, W) still works. If I unformat the references, I can get word counts again through the count at the bottom left.
Are you attempting to get the Word Count for the entire document or just a highlighted section? Are you working with Track Changes? If so, which Display Option (Final Showing Markup, Final, Original Showing Markup or Original) do you have selected? Do you see this issue if you try the same thing in a new test document?