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I've got a rather strong feeling that Windows' bootloader is installed in the MBR, and therefore the system is seeing that and never even getting a chance to check your /boot config.
Reinstall grub to the MBR instead of /boot (it sounds like your config file will be accurate the way it is), and that should fix things:
/sbin/grub-install /dev/hda (where /dev/hda is your master hard drive, presumably where both OS's are residing)
First, take a look in your /etc/grub.conf file to ensure that there are indeed sections for booting both Windows & Linux. From what you said earlier, I fully expect this to be fine.
Then, as root, issue the command:
got ur question, firstly u didn't need to install grub at MBR. The boot sequence of a i386 arch makes bios to search for the active partition of the disk. If the active one is found its boot sector/record is loaded and run. so instead u would have made partition with /boot active and ur problem will be solved.
in present case, u go to the linux rescue mode and again install grub. prefer at MBR, may be rewriting ur mbr will fix ur prob this time.
hoping fr the best