Windows 7: Hard Disk making Windows 7 Crash?

For some time now I have been confused by my motherboard main screen (shows motherboard type and a picture) which had started to take sometimes up to 5 minutes to bypass. Sometimes just because it was quicker i'd go through the motherboard BIOS and hit "Discard and exit" simply because it was quicker than waiting. I noticed that my secondary hard drive had something wrong with it. Something about the IDE controller would fail to work (according to the motherboard loading screen after exiting the BIOS).

In the past few hours I was attempting to copy something from my external portable hard drive to my secondary when Windows 7 crashed. After I rebooted I decided to error check the drive (ticking both boxes). I then proceeded to take a nap for an hour and when I came too, the desktop was back to normal with no Error check box. I thought to myself "Oh it must be okay then". I then noticed that the secondary hard drive was not showing up in My Computer.

I rebooted yet again and windows 7 began to crash. Sometimes at the windows 7 loading screen, sometimes upon logging in and other times after a few minutes of logging in. Each time I checked My Computer and although the drive was there, there was no information or little icon showing how much space is left.

After much annoyance I decided to pull the SATA cable out for my second hard drive and boot. Windows 7 loaded sweet as a nut and I have been writing this from the same PC.

Any ideas what's wrong with my hard drive? It is very useful for back-up, though, not so much now.

Try with clean boot
If it works as it should follow instructions
http://support.microsoft.com/kb/929135

If it does not work try in safe mode and report back.

I already attempted booting in safe mode (oops sorry forgot to add this to the original post).

Once again the same thing happened...Managed to log in but then Windows 7 crashed less than a minute after loading to the desktop.

Also should I try a clean boot, then once the PC shuts down ready to reboot plug my SATA cable for my 2ndry HDD back in?

Go to search, and type event viewer
Look for critical errors about the time of the problem

I have numerous cases of:
The device, \Device\Harddisk1\DR1, has a bad block. - Spanning almost 90 minutes. I think maybe from when I was attempting to check and fix any errors on the drive.

I also found quite a few: Crash dump initialization failed! - dotted about the place

As well as the occassional:
The file system structure on the disk is corrupt and unusable. Please run the chkdsk utility on the volume Media-BensPC.

Followed by:
The default transaction resource manager on volume Media-BensPC encountered a non-retryable error and could not start. The data contains the error code.

And some:
The driver detected a controller error on \Device\Harddisk2\DR2.

Seems like there are a number of problems
Run a sfc command
SFC /SCANNOW Command - System File Checker
If errors are found run 3 or 4 times
If not fixed and there are many we can do a repair install.
If not many perhaps we can just fix them

If no success with the above. Try a repair install.
Repair Install

Running the scan now. I was actually going to partition my hard-drive and make a clean windows 7 install this week (my week off). Maybe it's trying to tell me something.

Any ideas concerning my 2ndry drive? I still haven't plugged it in. Think it's ok or is it a case of a new brick to prop my door open? with

You can go to the website of the manufacturer and test it.

The scan completed saying: "Windows Resource Protection did not find any integrity violations". Hmm...?

OK thats good the OS is not corrupted in anyway.