If I partition a 160GB drive to 160GB, no Windows when installed there will boot. OK, that's annoying isn't it.
Here's the deal. Window 95/98/ME are DOS based and can't break the 127GB barrier as supplied from Microsoft. Windows NT4/2000/XP/2003 also from the CD have a boot and support issue as supplied from Microsoft.
Given what you've written, you have just reverified the problem.
Too bad you didn't note which OS since I could give the short version of the install onto such a drive.
Bob
done everything, copied files, added ATA card, windows will not boot from new hard drive

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic