Why do I lose data from serial port when I reboot my computer?

"This is caused by Windows opening the port at boot time for a very short time (under half a second). During this process, all of the serial ports are opened in order to detect input devices such the mouse.

The solution is to simply tell Windows not to do this, this way you don't lose your data since it's not being received. We can do this by modifying boot.ini and ensuring that we're using the /fastdetect switch. However, this will already be on in most cases, as it's enabled by default in Windows setup. I found the solution here, the article also includes informatation about NT and 9x (there are different solutions)."

There is also a command line tool available to disable scanning on selected com ports in the registry, if you want to avoid manually editing the boot.ini file.