Standard version of PHPed. I have a ftp user account that has its home directory set to the webroot that publishes just fine. I have a second phped project for the SSL directory which uses the same ftp account but is outside the webroot. When I use the Top Publishing directory field in the SSL project publishing setup its doesn't use the servers true root of /, but the accounts home dir as the root. The eval version didn't have this problem.

Could you please provide account settings, project properties and let know the directory you're expecting files to be published to?

ftp:account settings
host: 192.168.98.139
port: 21
everything else is left blank, except login and password

main html project
root: \\TWELVE\Website\html
account: ftp
top pub dir:

main ssl project
root: \\TWELVE\Website\SSL
account: ftp
top pub dir: /usr/SSL

The ssl project gets uploaded to /usr/home/usr/SSL in this setup, whereas I would like it to be uploaded to /usr/SSL.

You'd specify / as root directory in FTP account settings and adjust top pub dir in the project properties.
It works per following scenario:

if nothing is specified in the account, "initial" directory is used as root (what ever ftp initially shows in responce to pwd command)
if anything is specified, it will be used in initial CD command to jump to, and it will be root directory for account.

if nothing is specified in the project properties, the account setting will be used for root directory
if anything is specified in the project properties, it will be added to the account root.

Thanks for the explaination dmitri. It's all setup and running great.