Dear Andrew,
Are you using the "_yyyy" convention for the file name (for example: weather_file_1990.csv, weather_file_1991.csv)?
You also might try running the weather file checker macro on each file to be sure there is not a formatting issue that is preventing SAM from recognizing the file as a weather file.
If you have a way to share the files with me, I would be happy to investigate further. You can either compress them into a .zip file and email them to me at sam dot support at nrel dot gov, or email me a link to the files on a file sharing service (Dropbox or similar).
Best regards,
Paul.