I have a VPS account with root access. I'm used to being able to set file permissions using my FTP client. However, on this VPS account, my hosting provider has somehow disabled me from being able to set 777 rights on some folders and on some files.

I have root access so is there any way I can configure my vps account myself to allow me to use my FTP tool to change file permissions to what ever I want?

Do you have ssh access ? If so, change it through ssh.

if you have root access then go to your site and make sure fies youwant to change have admin privileges and not root or httpd or nobody

you can use: chowm -R newowner filename
use -R to force changes to all files at once in your folders

go back to your FTP and try to chmod