Hi JonathanC,
I would also try using the Sysinternals tool, Process Monitor to log the boot time activity of your computer.
http://technet.microsoft.com/en-us/sysinternals/bb896645
Here is a blog post from Mark Russinovich detailing how he used it to solve a slow login and another article that provides more info on its boot logging capability:
http://blogs.technet.com/b/markrussinovich/archive/2012/07/02/3506849.aspx
http://www.ghacks.net/2009/10/09/use-process-monitor-to-optimize-the-windows-boot-process/
You might also consider using the Logon and Services tabs of Sysinternals Autoruns tool to ensure that you are running as clean a system as possible:
http://technet.microsoft.com/en-us/sysinternals/bb963902
This tool should show more information than CCleaner (I could be wrong about that).
Please also run the following tools and let us know the results since MBR infections can cause slow boots (these infections cannot be removed with a re-format of the hard drive since the MBR is not written to during the standard format process).
You should backup any data that you cannot afford to lose before proceeding with the steps below since they can occasionally cause further issues:
TDSS Killer:
Download the Kaspersky TDSS Killer tool from here:
http://support.kaspersky.com/downloads/utils/tdsskiller.exe
Instructions on how to use it are here:
http://support.kaspersky.com/find?faq_id=2663
You might also find the following article on TDSS rootkits useful:
http://www.bleepingcomputer.com/virus-removal/remove-tdss-tdl3-alureon-rootkit-using-tdsskiller
Repairing MBR
If after the above steps, the issue of slow a boot up remains, I would suggest creating a new MBR using the Windows Recovery Console (I realize that you are using Windows 7, I have included the steps for Windows XP for reference only):
Windows XP
How to install the Recovery Console:
http://support.microsoft.com/kb/307654/en-us
How to use and the commands available in the Recovery Console:
http://support.microsoft.com/kb/307654/en-us
The command you will need is fixmbr
Windows Vista and Windows 7
The procedure for repairing the MBR using Windows Vista or Windows 7 is different from Windows XP, for information on the steps necessary, please see the following article:
http://support.microsoft.com/kb/927392/en-us
As before, start the computer and put the Windows installation DVD in your optical drive and boot from it.
Press a key when prompted, set the language and keyboard layout that you wish to use when the GUI (Graphical User Interface) loads.
Follow the steps mentioned in the above knowledge base article to open a Command Prompt window and type:
Repair the MBR
Bootrec.exe /FixMbr
Reboot the computer.
If necessary (i.e. the issue is still occuring), type the following command:
Repair the Windows Boot Loader
Bootrec.exe /FixBoot
If necessary, type the following command:
Repair the BCD (Windows Vista and Windows 7 only)
Bootrec.exe /RebuildBcd
If you encounter the "Bootmgr is Missing" error on boot up, you can instead use the following commands to resolve it:
Follow the above steps but substitute the commands after opening the Command Prompt window (using the boot from DVD steps mentioned in the above knowledge base article):
bcdedit /export C:\BCD_Backup
c:
cd boot
attrib bcd -s -h -r
ren c:\boot\bcd bcd.old
bootrec /RebuildBcd
-----------------------------------------------------------------------------
MBR.exe:
http://www2.gmer.net/mbr/mbr.exe
Download this program and run it as administrator. If the text file (.txt) file that it creates in the same folder as you downloaded this program to mentions any of the following text, you probably have an infection:
Copy of MBR has been found in sector
malicious code @ sector
PE file found in sector at [memory location within MBR]
-----------------------------------------------------------------------------
The steps details above should remove this infection if it is present, if not, please re-post in this thread.
I hope the above information is of assistance to you.
Thank you.