If there was a recent infection, and the company uses direct file transfers, then there's a strong chance that a file has been compromised, and is now infecting the entire network as it is shared. Dig into it, and you'll probably find which one. Either that, or it's spreading another way. Viruses don't die easy when they're able to spread on the network. There's a reason I disable all inbound/outbound connections to other computers when I'm at home.
Now, you might want to consider using something other than direct file transfers. One nice alternative would be torrents (forget their bad rep). When the torrent is created, the MD5 checksum is generated, and altered files (I believe) will change that checksum... which means the file shouldn't be shared across the network, and therefore would help to keep the infected files isolated. It would also have other benefits for the entire network's sharing platform, especially if a number of files are constantly being transferred regularly. Look into it.
I can't make any guarantees on enhanced security through torrents (as I haven't really looked into it), but it's definitely an option worth investigating IF you have a problem with regular sharing of potentially infected files. Also, contrary to popular belief, torrents don't need to be shared over the internet... so you can keep all files contained on your network. You can also just send emails with the checksums contained, the receiver plugs in the checksum to their torrent client, and the download begins.