Just cannot do a clean re-install

Trying to install a separate HD should not affect your Win7 installation unless you changed settings in BIOS. If it is a data drive there should be no BIOS settings changes needed - just make sure it registers. If it has a bootable OS then you can use the one-time BIOS Boot menu key given on first screen.

Try resetting the CMOS: Clear CMOS - 3 Ways to Clear the CMOS - Reset BIOS
Then try plugging SSD into another port, make sure it registers in BIOS correctly.
Check to make sure you have the latest BIOS update.

Your response to earlier suggestion to test RAM with memtest86 CD for 5-6 passes is that RAM is working in other install. You need to test your RAM with any problems like this.

Test each HD as well using maker's full diag/repair CD scan: http://www.tacktech.com/display.cfm?ttid=287 Then from the DVD Command Line run http://www.sevenforums.com/tutorials/433-disk-check.html on each.

Boot the Win7 DVD Repair console with only your Win7 HD installed, accept any offered repair, reboot to test if it starts. If not, boot back into Repair, click through to Recovery Tools list to run Startup Repair up to 3 separate times with reboots until Win7 starts. http://www.sevenforums.com/tutorials/681-startup-repair.html?ltr=S
 
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Hey, many thanks gregrocker, will do that and be methodical about it.
 

My Computer

Computer Manufacturer/Model Number
Intel Chassis SC5650WSNA
OS
Windows 7 Professional x64
CPU
2 Xeon X5650
Motherboard
Intel S5520SCR
Memory
Kingston 12 Gb DDR3-1333MHz ECC Registered
Graphics Card(s)
Nvidia Quadro FX1800
Sound Card
none
Monitor(s) Displays
Zalman Trimon 3D 22in
Hard Drives
Intel 160Gb X25-M SSD

additional storage: 1TB Baracuda 7200 12 Sata 7200 RPM 32Mb 3.5in
Case
Intel Chassis SC5650WSNA
Cooling
Intel BXSTS100A Active thermal solution
Put the HDD back in the machine and do a clean all "secure erase" that will over-write all the old Windows code and all other data on the entire HDD and leave it as unallocated space.

Have a look at Step One of this tutorial for an out-line on the wipe "clean all" procedure; be sure to post back with any further questions you may have and to keep us informed.



SSD / HDD : Optimize for Windows Reinstallation


I guess I wasn't specific enough about doing the wipe before Windows actually starts, as soon as you add the HDD boot directly to diskpart and do the wipe and when finished, then start Windows, my apologies mate, this is how I meant for you to do it.
 

My Computer

Computer Manufacturer/Model Number
* BFK Customs *
OS
W 7 64-bit Ultimate
CPU
Intel Q9550 Yorkfield
Motherboard
ASUS P5Q Pro
Memory
8GB Dominator 8500C5D
Graphics Card(s)
ATI : XFX 5870
Sound Card
Realtek HD Audio 7-1
Monitor(s) Displays
1x 47" LCD HDMI & 3x 26" LCD HDMI
Screen Resolution
1920x1080P & 1920x1200
Hard Drives
1x 80GB Intel X25-M G2 SSD : 1x 500GB & 1x 640GB WD Caviar Black(s)
PSU
Corsair 620HX
Case
Cooler Master RC-690
Cooling
Tuniq Tower 120, 2x 140mm and 3x 120mm case fans
Keyboard
Microsoft 500
Mouse
Razer Diamondback 3G
Internet Speed
14 Mb/s
Other Info
1x Koutech 3Gb/s SATA HDD Hot Swap Rack
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