About the only difference between a restart and a start after a shutdown is that the power supply does not get cycled. MB, mem, cpu... all retain power. Software-wise, everything stops and starts anew.
Where exactly in the startup cycle is the extra time being taken? Try running procmon.exe [from winternals] - enable boot logging, reset the filters, and restart the machine. Examine each type of activity [reg , file, network, process ]. See where the time goes.
Malware staying live in memory...? I don't know... try Autoruns from winternals. Run gmer.exe to check for rootkits.
You leave open a lot of possibilities.
http://technet.microsoft.com/en-au/sysinternals/default.aspx
[chkdsk pretty much announces itself when it runs]
gerbil
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I've had a similar problem on a company computer before.
It ended up being a driver issue. We were using some old ID scanners that were built for Windows 98 and the drivers were terribly ported to XP by the sales guy (they were really cheap).
So every time the computer was rebooted, logged off, etc, the drivers would hang up the system and you would have to go into Task Manager and kill the process in order to logoff or reboot (unless you wanted to wait several minutes for the logoff/reboot).
Not sure if that has anything to do with your problem, I'm just saying there's a possibility that it could be driver related.
donkey_pasta
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So it is not softwares that are being prefetched. [And yes, prefetch folder entries would be rebuilt with entries for softwares you used during the sessions after deletion]
Try using selective startup via msconfig to isolate the group causing the problem. I could type all day, but M$ tell you how: http://support.microsoft.com/kb/310353
Restore to before the networking experiment?
gerbil
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During the reboot cycle how long does it take to turn off compared to the time it takes to boot up?
Try unchecking all the items in msconfig startup and see if that does it.
Also, I've see some system services be more aggressive than others -- so even if you deselected it in msconfig something may be causing it to start.
I'm really curious to see if it takes a really long time to shut off during the reboot cycle or if it takes a really long time to boot up. My guess is it takes a really long time to shut off and if that is the case then there is a program hanging up.
Do you get any kind of error messages or messages asking if you want to "end 'blank' program now" when you reboot?
donkey_pasta
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