I sorta' have the same problem. two weeks ago i had updated my hard drive to a seagate SATA, i have installed winodws and it worked great. last night i tried to install mandrake 10 but during the install it couldn't find my hard drive, it did give me the option to view my hardware list and install an optional driver or module. i had tried several and none worked. I had also tried using Fedora core 2 and it did'nt work either. I am going to down load fedora core 3 and try that.
What i think the problems you are having is that linux cannot see the SATA drive so it makes your other drive the master, and this is were it installed the boot loader. becuase your SATA drive is realy the drive it boots from and the windows NTLDR has no entry for linux it just boots winodws. what you can try and do is go into you bios and change the boot sequence or disable your SATA. you will want it to boot to the IDE drive first. This is kinda' a pain but should work.
this is one workaround, another is to use you NTLDR to boot linux, it is kind of complacated but it will work rather slick. I am looking deeper into the matter to find out how i can use my SATA drive for linux. Hope that helps
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