I'm assuming that you are referring to a menu that is a list of operating systems that Windows is offering to load.
If so, It's nothing to do with the MBR, the board or the hardware RAID.
Windows XP uses the file boot.ini in the root of the boot drive to control the list that you re describing.
The items for the list each have a line in the [operating systems] section.
The default= line controls which entry is selected if the timeout specified in the timeout line reached (or there is only one operating system)
Hence you could delete the line referring to Windows setup and change the default entry to refer to the correct OS entry.
Boot.ini can be edited by hand in notepad or from the startup and recovery options in Windows system properties...., but if you get it wrong you could render your system unbootable. Only try this if you are 100% confident that you understand how the boot.ini file works.