You must make sure that SeeYou is the only application running at that time as only one application can access the COM port at the same time. You must shut down all applications accessing the COM port. This includes Active Sync (for PocketPC), HotSync (for Palm), LXe (for LX Navigation instruments) and similar.
Active Sync must be disabled on the COM port which you are trying to use for Communication (Active Sync > File > Connection Settings > uncheck Allow serial cable )
If that doesn't work, please create a "logs" folder inside the SeeYou20 folder (by default it is in c:\program files\naviter\seeyou). Try to communicate and send us any logs that are created in there.