Missing Index in News Sources
After digging around I just found an interesting tidbit about why - sometimes - the index in the Kindle files for news sources is missing:
It sounds like you are getting the book reader, and this would be because the EXTH[501] field of the metadata is not set to NWPR (for newspaper). The latest release of calibre fixes this. HOWEVER, if you email the mobi to your Kindle, Amazon will overwrite the EXTH[501] field with PDOC which will put you back to the book reader. If you transfer the mobi via USB it doesn’t get overwritten and you’ll get the news reader which is what you obviously want.
There doesn’t seem to be any way around the email issue. Unfortunate, but “that’s progress” I guess (sarcasm).