Interesting booting issue

What step startup Repair can you get to?
Startup Repair

Step 4. The tool finishes operating in 3 seconds and I get the window shown in step 4.

There is something wrong with your 100mb System partition which doesn't have normal markings but is labeled "EFI System Partition" as it might have been from the factory.

But it isn't booting Win7 now judging by the fact that it shows empty.

You can try to rewrite it by marking it Active in Disk management then Run Startup Repair up to 3 separate times with reboots. To be sure I would also delete, recreate and format it as a 100mb Primary partition marked Active before running the Repairs. Back up your files first and unplug all peripherals and other HD's.

When you reinstalled, did you boot the Win7 DVD to use Custom Install, then use drive Options to Delete all partitions, Create New then Format before install? This would issue a new 100mb System Reserved partition which should load correctly upon install to the adjacent OS partition you create.

If not, I would try it this way.

Here are other tips for getting a perfect reinstall - use the ones which apply: Reinstalling Windows 7

Reboot at step 4.
Are you using the Startup Repair CD or Windows 7 DVD?

It is formatted FAT which is not optimal for a Win7 reinstall. It would be best to delete it and recreate it Primary NTFS Active:

Boot the Win7 DVD or Repair CD, press Shift + F10 at first screen to open Command Prompt, type:

DISKPART
LIST DISK
SEL DISK 0 (confirm this is WIn7 HD first)
LIST PART
SEL PART 1 (confirm this is 100mb)
DELETE PARTITION OVERRIDE
CREATE PARTITION PRIMARY
FORMAT FS=NTFS LABEL="System Reserved"
ACTIVE
EXIT

Now close Command Box, proceed to Repair console to run Startup Repair up to 3 separate times until Win7 starts on its own.

Back up your files first as these operations can fail, unplug all other HD's

Alt method: You can use free Partition Wizard bootable CD to delete 100mb, create new Primary NTFS marked Active.

Sounds good, I'll try it and then report back. Thanks.

Deleting 100mb partition not needed. but you can.
Reboot at step 4 of
Startup Repair
Note: You may need to do startup repair 3 to 4 times.
Startup Repair - Run 3 Separate Times

Alright, here is a major update on the issue:

1) I tried gregrocker's tip and it was critical. Deleting that partition made Windows completely unable to boot, I had to reinstall the whole thing. I don't mind it though, as my main data was luckily located on my other drive and also I wanted to check if reinstalling actually solves the problem or not. Well, it did not.

2) But, I found out a lot of things that could lead us to the solution (if you take your time again to read this , which is greatly-greatly appreciated). First of all, formatting my main drive did not do anything. My current installation is on a freshly formatted disk and everything remained the same.

3) The conclusion from the previous two facts is that the 100MB partition for some reason always comes with the fresh installation of my Windows 7.

4) The oddest (is there such a word? :O) thing of all though is that even with Windows uninstalled and my drives removed from my computer I still see the Windows Boot Manager option in my BIOS (although obviously when I tried to boot form it it did not do anything). Is it possible for an OS to integrate itself to the BIOS, therefore to create a relation between them?


I hope this additional info will bring new ideas. Thank you for helping once again.

Hello?

Did you not read the steps I gave you to recreate the 100mb System Reserved partition, mark it Active and then run Startup Repair up to 3 separate times to write the System Boot Files to it until Win7 starts?

Why would you think Win7 would boot after deleting it's 100mb System Reserved partition and then just ignoring the other steps given to recreate it?

The 100mb System Reserved partition is created when installing on a blank HD, or when the installer is booted to use Custom install Drive options to Delete all partitions, Create new ones and format before install. It's benefit is that it conveniently places the Repair Console normally only on the DVD or REpair CD on the F8 Advanced Boot Options.

In your case you did not delete the partitions before the reinstall and a strange factory EFI 100mb boot partition remained which was not in use (empty) but there was no System flag to tell us what was booting Win7.

The solution is to recreate the 100mb System Reserved partition which we pioneered doing here in these forums scores of times, by creating a Primary NTFS partition (yours was FAT), marking it Active and running Startup Repair up to 3 separate times with reboots.