Windows 7 "pausing" on boot/ sleep mode restore

I posted this on the hardware board but it could be a software issue too.

I've been having an intermittent problem for a couple weeks but now it seems to be happening all the time.

When i first boot my Windows 7 Ultimate (64bit) system, after logging in the hard drive reads for a second or two. It then stops for 3-4 seconds like it’s paused and then reads again. This goes on for 10-15 minutes then suddenly starts reading functioning normally. When it's "paused" I can move the mouse but can't click on anything. BUT if I do click on something when it resumes running for those few seconds it'll complete the operation.

Before it was just when booting now it seems to do it every time it comes back from sleep mode. I've looked around but can't find anyone with a similar problem. I'm running a WD Raptor 150GB HD. I've scanned it and it comes back perfectly fine. I noticed last night the problem also effects the second physical HD in my system. If I click on a folder it won't open until the "pause" is done.

I'd love to get some ideas about what is causing this issue.

 

Any yellow ticks in 'Device Manager'? It might be looking for drivers. Disconnect any peripherals and see what happens. I've always had an issue with trying to wake it up on both my desktops and killed it in 'power options' as I run 24/7 anyways so I don't really care. You have a laptop where it is more important?

 

First things first:

• Check for a BIOS update.
• Check Device Manager for any exclamation marks on devices, and if so, download and update drivers.
• Run ChkDsk
• Defrag possibly

 

I already checked all those places unfortunately. Everything appears to be fine. HDD was 1% fragmented when I ran it. Also checked the msconfig and removed almost everything from startup. I also ran Ccleaner for files and registry errors. Did all the updating I can on the system still having the same issues.

 

Shot in the dark but try opening Task Manager when it's running and setting it to order by cpu usage. Might give some clue.