My first thought on debugging would be to log all of the incoming/outcoming communication and check the logs as a way to verify what is actually being sent and received. I didn't see anything in Win32::SerialPort's documentation or the documentation for Win32API::CommPort (which Win32::SerialPort is based on). The logging options are clearly documented for Control::CLI, which uses Win32::SerialPort on Windows for serial port communications. If you don't want to switch over to use Control::CLI, you can check out its source code to see how its doing the logging.
My next thought would be to look at timeouts and buffering. For the timeouts aspect, check out the last portion of the Configuration and Capability Methods section of the Win32::SerialPort documentation. It's been a long time since I worked on code using Win32::SerialPort, but I remember having issues related to timeouts.