The fact that you can connect to the FTP server and can upload files before losing the connection indicates that it is *not* the OneCare firewall causing your problem. If the OneCare firewall were blocking the connection, it would fail to connect to the server with no connection available. The connection and the file upload use the same port/protocol, so the fact that it starts and works for some files means that the OneCare firewall is correctly configured. OneCare would not allow the connection for a time and then kill it or block it.
You can confirm that OneCare is not the issue by opening OneCare and clicking on Change Settings, then disable the firewall. Make your FTP connection and upload the files. If it still fails, it isn't the OneCare firewall, If it is successful, repeatedly, with the firewall off, I'd be surprised and would then agree that the OneCare firewall is playing a role in the problem.
As for the msmpeng CPU usage during the transfer, there may be a conflict causing this or it may be normal. msmpeng is indeed the scan engine, so as the files are accessed for transfer, they are being scanned. I don't know that I'd expect 25% CPU usage by the scan engine, though, unless something else was at play causing a deadlock with msmpeng when it is trying to get access to the files for the scan. If you have no other security software installed/running, you may be able to workaround the issue by going to the virus and spyware tab in Change Settings and setting an exclusion for the folder containing the files you are going to be transferring. That way OneCare won't scan that location.
Of course, the best thing to do is determine what may be causing the conflict. It may well be that both issues are being caused by the same thing. You may want to contact support to have this investigated.
How to reach support (FAQ) - http://social.microsoft.com/Forums/en-US/onecareinstallandactivate/thread/30400b52-7f26-4ba0-bc18-17e305329d90
-steve
Microsoft MVP Windows Live / Windows Live OneCare & Live Mesh Forum Moderator