Such as some USB thing plugged in to something the scans didn't find. My old Acer ter600 after fair too many tweaks could never boot in less than 4 minutes. One day by chance I ran a SCANDISK (not in XP or later!) and it was twice as slow as my new laptop. I ordered a newer drive, cloned the drive and the next boot was 2 minutes.
No scan ever told me the HDD transfer rate was on the slow side.
This is not to say this is your issue but a story I share.
Scan like Grif notes at http://forums.cnet.com/7726-6132_102-5098912.html?tag=posts;msg5099421
And be sure no USB things are plugged in.
I have a Dell Inspiron 1545 laptop running Windows 7 64-bit, 2gb ram, and a Intel Core Duo 2.20 GHz processor. It takes an average 5 minutes between pushing the power button and loading the desktop. At this point I think it is either a bad motherboard, bad hard drive, or other defective hardware. I ran both Super Anti-spyware and Malware bytes, they found nothing. I checked for updates and cleaned the registry. I've gone through msconfig and removed unnecessary processes. Using msconfig I double checked that it was using both processors. I also uninstalled any unnecessary programs. Finally I performed both Windows and Dell hardware diagnostics. Everything passed as fully functional. So I'm left with the final question, what would be slowing down the boot so much? One important note is that Dell boots with normal speed. It's when it starts loading windows it slows down so badly. Once it is on it runs very slow. Any ideas on what I'm missing?