is analyse how long each component of windows takes to boots?

Have you tried replacing the ethernet cable or switching the PC1 with the PC2 to see if the results stay constant or vary?

Re-seat the RAM.
Test hard drive.

Same power supply?
A PSU that is putting out 'dirty' power will slow things down too.

This is a "Process Monitor".....it will better give you an idea of where it is taking longer compared to the other computer and will allow you to see where the problem is:

http://technet.microsoft.com/en-us/sysinternals/bb896645.aspx

Hope it helps you.

I've improved the boot time on Machine 1 (similar time machine 2) by plugging the hard drive into SATA port 1 instead of SATA port 0 on the motherboard.  Not sure what could have changed by plugging the harddrive into SATA port 1 instead of port 0.  I have re-imaged the slow machine and plugged the HD into port 0 (the slow port) the machine boots up with a good time again, weird.  Does anyone know what the cause of the problem could be?

I was pointed in the right direction to the problem using bootvis.  It reported that the disk IO was slow on machine1 compared to machine2.  (It looks like the tracer code for BootVis has been taken away because disk IO is the only metric thats collected.).  Anyway this led me to change the SATA port.  

These are 2 programs that will monitor the boot process and record extra detail about the boot process. not used them because i already found a solution to the issue but may come in handy.  Free 30 day trial for both softwares  

http://www.greatis.com/utilities/bootlogxp/
http://www.clockmod.com/index.php?/products/view/winbootinfo_1.0/

rightio  i'll check it out.

sorry i think you mis-understood.  

1. Before the re-image I plugged the HD into a different SATA port (port1) and the machine booted up at a faster speed.  
2. i plugged the machine back into the orginal port (port 0) and the machine went back to its old ways and was slow at booting.
3. I re-imaged the machine and now get a quick boot.  The SATA is still plugged into the supossly slow SATA port (port 0).  

no changes in the BIOS.  No changes to Windows, well known to us, must have been automatic if there was (users do not have admin access).  I can not explain why or what has changed.  I imagine after time the new port (port 1) will start to boot slow.  

Yes - your on the same thought process as me.  I also beleive something has changed wtihin Windows (like you said its the only dynamic part), I know users dont have Admin rights to change drivers.  I even tried to roll back the device drivers but it says no previous drivers to roll back to.  Also tried un-installing drivers and letting Windows re-detect and system still runs slow.  

When the system is in its state of slow booting (plugged into SATA port 0): the computer will boot fast in safe mode.  Also if i change the HAL to the basic HAL (standard from ACPI multiprocessor PC) the system boots fast.  A little more info for you guys.  Im still bamboozled to the cause and what triggered it.....

Don't give it to much thought..... it's all about 0's and 1's..... any minimal corruption in the registry....a little flicker of the power and you get a "1" instead of a "0" and the whole registry setting is messed up.....

was it on DMA ?

Ive checked the DMA (just needed a bit of time) and taken the settings from Device Manager when the port is plugged into the different SATA ports.  

Secondary (2st in list)  - This is the faster port (0)
Device : 0
Device Type :Auto detection
Transfer mode : Auto detection
Current transfer mode : Ultra DMA mode 6

Primary (2nd in List) - This is when its plugged into the slower port (1)
Device : 0
Device Type :Auto detection
Transfer mode :DMA if availible
Current transfer mode :PIO Mode

So it looks like the PIO Mode is slower than DMA mode 6.  Ive also checked the recently re-imaged machiens and they are using the transfer mode : Ultra DMA mode 6.  So something is changing this over time. Interesting....Any ideas?  

did you reset it, as described in the links?

yeah I ran the script from http://winhlp.com/node/10 and it worked a treat.  We have 70+ machines its happening on and we're not sure why its occuring?  

What we are putting in place is for landesk to retreive the registry settings into its database and then reporting on which machines have the issue on a daily or weekly basis. then running the script on the affected machine.  Any recomendations/ideas welcome?

thanks guys your help is much appreciated.  It took a while to find this issue and caused us a lot of greif!  Cheers