Just wanted to give an update. I finally figured out the problem. We had recently upgraded our Net Nanny before all these problems with uploading began although I kept turning it off when I published so I originally didn't think it was an issue.

Turns out that just disabling wasn't enough and I had to go into the Applications Override section and add the BlueVoda.exe, BlueFTP.exe and SmartFTP.exe to the override. That did the trick. I still need to turn off my Zone Alarm firewall when I upload so I try to do little bits at the time so I'm not totally vulnerable while uploading.

Normally I've found the BlueVoda folks to be extremely helpful in figuring out issues, but there were a couple on my support ticket that were borderline rude.

And the fact that some of my other threads on here were disappearing is a bit concerning as well.