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This is a fairly common problem on Apache, because Webmasters incorrectly specify their custom error documents using a canonical URL like:
ErrorDocument 404 http://www.example.com/error_page.html
ErrorDocument 404 /error_page.html
It's wise to check your server's response to missing, redirected, and forbidden pages using something like the Server Headers checker [webmasterworld.com].
Jim
Your "404 page" does return a status of 404, doesn't it?
This may be a factor. I complained to my host about this about a year ago - I don't think they understood the problem - it didn't get fixed. I decided to add NOINDEX to my 404 page about a month ago. HOWEVER, at some point, my host did indeed fix this problem, my 404 page DOES return 404 now not 200. I checked just before posting.
Kaled.