Hi,
As there is no native way to automatically check in Log4OM a callsign selected in FlDigi, I've wrote a small script in AutoHotkey, a open source automation scripting language for Windows, you can find more about it at this page:
https://autohotkey.com
My script is open source and available at this page:
http://bit.ly/FlDigi2Log4OM
If you need some help, feel free to contact me.
73 de IZ3XNJ Stefano