What they've been trying to tell you is that Windows will not / is not able to boot from a logical partition, and now you seem to have made the "System" partition (the partition that contains the Windows boot files) a logical partition; you seem to have just shot your-self in the foot.
I would suggest unplugging the 2nd hard drive and then try installing. If successful, re attach the 2nd HDD
Because I was not clear, I will recap in case anyone else has the same type of problem.
I thought that maybe there would not be enough primary partitions available (and I had read the the 100 MB partition was not necessary), so I changed the original system to boot from the OS partition, verified that the computer still booted, then changed the original 64 bit 100 MB partition to logical (I did this because I was concerned that the new Windows install might want to create *two* primary partitions, a System and an OS; it turns out the new install did not create the extra 100 MB partition.)
So after unplugging the other hard drive, the new OS installed immediately and painlessly. I just couldn't believe that this could be the problem(!).
I hope that was a little bit more clear. Thanks to everyone for their assistance.
My apologies, I did mis-read your last post.
I'm glad to see you have found a solution thanks to tw33k and thanks for the update.
Have a look at Option Two of this tutorial at the link below to recover the 100MB partition space into the Windows partition if you choose, obviously you won't have to be concerned about the startup repairs now.
Partition Wizard : Use the Bootable CD
Unless you were planning to install 7 on the second drive and make that one a stand alone self booting drive you wouldn't need to unplug it if seen as Disk 1 and the first seen as Disk 0. The Windows installer will automatically default to the first drive for seeing the boot files and mbr information placed there.
As for the 100mb system reserved partition the Windows installer creates that on it's own if the drive is raw and unpartitioned. For simply seeing 7 installed without that present you have the choice of the 48gb primary seen on the first drive or lose the 500mb partition on the second for setting up a dual boot.
The image here shows what is seen on the 100mb boot partition when a drive isn't already partitioned and formatted and the MS drive tools included on the 7 install disk are used. Note after restoring a drive image to the second drive for running the beta versions there I assigned a drive letter to the 100mb in order to view just what files are placed there during the typical install to an unpartitioned drive.
Note the 48gb second primaty seen on Disk 0 is large enough for an install but you may also find that to be a bit cramped once you start installing numerous programs as well as downloading files and utilities to run there.
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