I guess the problem/s you are having aren't quite clear.
From your first post it sounds as if:
1) you have 32-bit Ubuntu installed and are trying to install 64-bit Ubuntu as well to dual-boot (Ubuntu/Ubuntu)
2) booting from hard drive causes problems
From your third post it sounds as if:
1) you have Windows installed and are trying to install Ubuntu on a second hard drive to dual-boot (Windows/Ubuntu)
2) booting from CD causes problems
I think part 2 is what is causing the confusion. If you are having problems only with the CD then you may simply have a bad CD. Have you checked the CD for errors (boot menu option)? Does the CD work on any other computer?
could I install ANY linux OS through windows onto a separate hard drive?
Not
through Windows per se, but you can install from a FAT32 drive (and even do a network/internet install). That method is a little more involved though, and it would be easiest to install from a proper CD/DVD.