As Peter said. Have you reloaded firmware?

I know you said that you tried other PCs. Have you tried uploading? Does that work? If so, it's most likely not the remote. Also, are you downloading with the USB cable attached to the DS with power attached, or directly to the remote. Is your battery fully charged? Battery level may have something to do with this.

RE Connectivity...

When you connect the pronto, under USB Devices in My Computer->Properties->Hardware tab's Device Manager, does the Pronto Driver show or does it show Unknown Device?

If it shows Unknown Device, then you should search for +Potential +USB +Issues and follow the links in the thread I posted to reinstall the USB drivers.