Massive boot delay after altering partition layout

I recently reformatted my Vista install because boot time started to take a very long time (went from an average of seeing the green bar go by 8 times to around 40). I couldn't figure out why this had happened before I reformatted and I just assumed it had something to do with having personal programs being started at boot time and maybe a hint of fragmentation.

In a previous thread I had this similar problem occur after I had defragmented using 3rd party applications. (for the record, I have used a different defragmenter on every reformat I've done and I've had this problem with PerfectDisk, Diskeeper, and O&O. And as suggested by someone in this thread, Vista never rebuilt its 'tracing files' even after a year of keeping that install.)

Anyway after I had reformatted and installed all of my applications, boot time stayed at around 9 green bars, so I ignored my theory about applications slowing down my boot time. I then tried defragmenting with Vista's defrag.exe using 'defrag c: -w -v' and boot time increased by about 1 or 2 green bars, so no big deal.

I then decided I would try out Windows 7 and reinstall BackTrack and seeing as I already had 3 primary partitions I created an extended partition with a logical NTFS and ext3 partition. As soon as I rebooted after making these changes boot time jumped back up to around 40 bars passing by like my previous install and hasn't gone down since.

I had a feeling that this would end up happening so after I had reformatted, I installed all updates and then created a compressed image of my Vista partition using Partimage (it only makes an image of the used space). So at least if I decided to 'reformat' I could just restore the image and I wouldn't have to sit through the Windows install screens and reinstall service packs and other updates.

I doubt there's a fix for this so I'm posting this as more of a discussion; has anyone else had similar experiences?