I might be stating the obvious here but using GPL licensed software and making changes and using them internally (like within a company) is okay. Google, Yahoo, Amazon and other companies does this and this is not a violation of the GNU GPL license. Also providing a hosted service such as hardened FTP server space (with patches whose source code is not available) also does not fall under the purview of the GNU GPL license. It is perfectly legal to do that.
It is only legal if the original package is licensed under the GPLv2 or earlier, which obviously it is. The GPLv3 tends to look at it differently as of now.
Regards, Debarshi