Seems to be OK. I would not call it a bug in Windows. It probably can even be avoided by tweaking MPTray or the SplashScreen a bit. I would reword it in a more neutral way. Something along the lines of "Windows default notification behavior".@Scythe42 - can you sanity check my wiki input please:
http://wiki.team-mediaportal.com/1_MEDIAPORTAL_1/13_Setup_Guides/2_Startup_MediaPortal/Green_Button
In general the the task bar flash feature (I have no clue how MS calls it) does not always place nicely with fullscreen applications launched by another application and not by user input.
"ForegroundFlashCount defines the number of times the taskbar button flashes to notify the user that the system has activated a background window. If the time elapsed since the last user input exceds the vale of ForegroundLockTimeout, the window will automatically be brought to the foreground."