These are error messages from the serial driver indicating that incoming data was lost. You should be able to trap overrun and data framing error events in your app. This might be related to the issue we're working on with you in topic 1368.
When the debug port shows the LSR_xxx messages ReadFile returns a timeout. I have increased the timeout value with no change. I have tried to trap the errors using both ClearCommError and WaitCommEvent. Neither indicates an error. Any ideas on how to trap these errors?