When I try and do a smart sync upload the new file is not being uploaded. The transfer log says it was uploaded but it's not. Looking at the timestamp on the server shows the old file and the program changes are not there. The server and I are on the same timezone so that's not the issue. Where else to look?

Please check account settings and "root directory" in particular. If you set for example /www/xxx as the account root, and /www/xxx as a remote root for publishing in the project settings, the final target directory will be /www/xxx/www/xxx/. In other words, project works with a subdirectory in the account's directory tree.