Well, I thought 3 seconds fixed it but the error timeout returned. The PC is running fine (Windows 7). I defragged and ran malware, spyware and it came up clean. I'll put the polling back to 2. I wasn't transmitting at all when it happened. I was going through my log and just listening to 40 CW when it happened again.
Update 12/31/2011: I am logged into a local node using Telnet1 and have been listening to ZS4L on 15 meters for the past hour and the timeout message has appeared a dozen times. I've had to reset the radio each time. The pc has been defragged several times and is running fine, I ran maleware and spyware (nothing found).
The STOP BITS is set to 2 for the FT-1000D and the POLLING INTERVALS is set to 2.0, BAUD RATE is set to Ø (default). All the cables to the radio and CAT interface have been checked and are secured.
I am out of ideas what might be causing the timeout error to appear so many times