Server Issues Anyone have Ideas?

[jhannawin]

the server ran Linux

Great, that means there'll be easily accessible log files. Assuming your site is backed up, going through the backups and extracting the /var/log directory would give you a great place to start some forensics. If you are not technical, find someone who knows Linux and ask them to take a look. You mentioned 'ftp'? That's where I'd start

[commodityman]

Thanks for the advice, but I have to agree the same was going on, i.e fishy to me too. I had the dedicated server through my web design company and I never talked to the hosting company, the one hosting one of my domains. I think they said some of the crap to boot the domain out and I have another hosting company now, all infected files are removed, ftp uploads are always secure, software protection is now installed, and I will see what happens from here.