filtered HTML files

I have two computers one with MS Pub 2000, the other with MS 2003. I upload simple web pages created with these programs.
Pub 2000 saves the data as separate files to upload and works fine. PUB 2003 creates "filtered HTMLfiles" which should be quicker but will not complexly upload using the same settings-not all of the pics are uploaded correctly and Smart FTP just says it can find all the files.