Just telling my success/sob story in case it might help somebody else
I'm relatively new to Parallels but mysteriously found I'd lost the ability to boot Bootcamp. This occurred after my battery ran out... but I had also installed several pieces of software, so I had no clue what the source of the problem was.
Being the wise dork I am, I backed up the Bootcamp partition using Disk Utility (bad move!!!) and Norton Ghost to a Mac External Drive.
My goal was to get bootcamp going again because I need to run software that hits the graphics harder than Parallels allows. So as much as I love Parallels, I still needed Bootcamp bootable.
Difficulty #1: Bootcamp 1.3 Beta and different size partitions
I did not read these discussions before I reconsolidated my Bootcamp Partition and upgraded to Bootcamp 1.3 beta at the same time. Oddly, I found that unless I make a Bootcamp partition with the preset 32 GB NTFS setting, I would get a HAL.DLL error during installation, as it seems Windows would try to load from the smaller hidden (?) partitions that Bootcamp makes, and HAL wouldn't be there - the jerk!
Booting into MacOSX showed HAL.DLL to be in the Windows partitions - hence the conclusion above that the installation process was trying to boot from the wrong partition. This did NOT happen with NTFS at 32 GB as preset in Bootcamp.
Difficulty #2: Windows Reactivations
I do not know when Windows wants to reactivate versus when it does not. have a university volume license disk that I slipstreamed and it started complaining of being activated too many times. A call to Microsoft solved that, but it seems to only allow itself to be activated on Bootcamp OR on Parallels, but not on both. Wah!
I ended up reverting to an older install that did not give me the reactivation woes.
Difficulty #3: Interrupted Install
I tried interrupting the install once the partition was formatted, thinking I would simply copy back all of the files (NTFS partitions are writable after installing MacFuse and NTFS-3G - which of course I needed to update MacFink for, and then when the packages weren't on MacFink, I had to compile from source AFTER updating the developer tools, sigh).
I then copied everything from my drive image over to the newly formatted boot partition as per this article:
http://www.macosxhints.com/article.php?story=20061025130528687 AND IT DIDN'T WORK!!!
Booting with Norton Ghost Rescue shows some kind of Install partition - my guess is it is the EFI versus BIOS boot methods... so even after restoring the original disk info, neither Bootcamp NOR Parallels would boot. To remedy this I had to go back one again and consolidate partitions, make a 32 GB Bootcamp partition and fully install windows.
Difficulty #4: Even after reinstating the failing drive contents, still no Bootcamp Boot
When I finally had the Bootcamp partition back AND with a fresh install of Windows, I still didn't have all my applications, including an activated version of the latest Office - like I'm going to let that die with my windoze install. So, I backed it all up using Apple's Disk Utility and then used Ghost to restore the drive I originally had - the one that would not boot into Bootcamp, but would boot in Parallels.
Now, I was wiser having read these forums to discover some other files were important, namely the ones mentioned in the boot line of boot.ini that parallels uses.
SO, under MacOSX, I mounted the backup of the working Bootcamp image, and copied HAL.DLL, NTKRNLPA.EXE and NTOSKRNL.EXE to overwrite those that the failing Bootcamp partition was trying to use.
In the kerfuffle, not only had HAL.DLL become identical for the paralells AND Bootcamp disks, but so had these two Kernel files, Replacing with known working ones (fully patched for windows security crap of course) allowed the system to boot without a hassle. Other files in Windows\System32 had been modified by running parallels (as one can tell by looking at date modified), but I did not touch them. Note that the c:\boot.ini should also not refer to kernel files ending in _.exe as this indicates a boot into Parallels, using the modified Kernel files.