Well, maybe it's a hardware detection problems. Try to check ur IDEs are in good condition or not (sometimes an minor damaged IDE may still acting normal.
IDE device initialising error may delay the boot-up process (experience before with prob. IDE attached with CD-ROM....takes about minutes to boot into windows)
If no any hardware errors, it's may coz by loading anti-virus software which will scan ur system and slowed down ur boot processes.
Could U point out the prob. more detail, do U reinstall the windows and the prob. still exist ?
Or u may try boot-vis from microsoft downloadcentre
this tools enable U to observer every booting processes and it can help U to optimize ur boot up speed (I tried and it's works !)
40seconds to 49seconds for booting into windows and become idle (my records).
Use some registry cleaning software. This will help U to clean rubbish registries.
I've this prob.t before. I hope this could help U ! :wave: