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Check your BIOS settings: My Gateway system is set to boot a MiniNT in a small FAT partition which checks for the "correct" MBR in the other partition. If it doesn't find it, it starts the "recovery" process.
I think you can change your BIOS settings so it boots from the first partition instead of the MiniNT one. My Gateway laptop is a MX6436 with XP (not Vista), so I just set the C:/boot.ini file to let me boot Fedora if I wished. I not sure if Vista supports booting non-Windows OS, although I think I've seen some "How-to" comments about doing so.
So, if Vista does support booting non-Windows OS, you've got two options:
1) Bypass the MiniNT boot (i.e., make partition 1 active and set the BIOS to boot to it) or
2) Set the Vista boot loader to let you boot to Linux as well as Vista.
Note: Per GrueMaster's comment, Fedora Core 4 is not even a supported distribution. The only currently supported Fedora distributions are Fedora Core 6 and Fedora 7, and support for FC6 will be terminated fairly soon.
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