I used WinClone to backup my Bootcamp partition, which was a Windows 7 Ultimate install, on my late 2006 Macbook Pro. I desired to expand the Bootcamp partition's size. It worked reasonably well with some hiccups along the way and some remaining issues.
Bootcamp Assistant utility would not recreate the partition. This was due to a lack of contiguous space that is required for the Bootcamp partition. As a result I wiped the whole drive and reinstalled Snow Leopard, did the minimum amount of system updates, and created and formated a new Bootcamp partition. WinClone restored the image without complaint and the image was automatically resized to the new partition's size.
The first thing I noticed was that instead of the newer "slick" startup screen (4 colors wisping around, a Windows 7 title), there was more of an old school style startup screen (a progress bar with block increments, yellow/greenish color, nothing else really).
The initial bootup to a login screen was slow, perhaps as Windows dealt with the partition changes. After logging in, the screen goes blank and the computer seems to hang for a minute, before completing the login.
After subsequent restarts, the slick screen is still missing, boot to login screen is normal, but the time from login to desktop active is still very slow. As a side note, this behavior of a long time from login to the desktop finally loaded I've previously only seen when the computer would try to hibernate and fail (battery is really bad). On the next startup, I would see this behavior, but not subsequently.
So a potential cause: I imaged the partition after hibernating out of Windows. From reading some posts/guides on the subject, this was not recommended, and perhaps shouldn't even have worked? Could the partition be stuck in some weird mode as a result that makes the boot issues appear?
I've attempted to disable hibernation and restart, trying to delete the .sys file that hibernation uses. Other fixes I'm thinking of attempting are booting a Win7 disc and repairing the install/partition. I can't shake the nagging feeling something isn't right as a result of the modified boot screens and the slow login process.