If you clean reinstall Windows 7 with the disks, why would you expect your programs to still be there?
What you need - and I'm sorry it was not mentioned earlier but we were under the impression you wanted to run Factory Recovery - is to run Startup Repair
repeatedly from the System Recovery Options.
A problem can be that if GRUB is on the HD it may corrupt Windows 7 beyond repair until GRUB is wiped completely. This is the point Theog was trying to make.
If Startup Repair can't get any traction after several attempts, make sure Windows 7 or it's 100mb System Reserved partition (preferred) are marked Active, then run Startup Repair - Run 3 Separate Times
to repair/rewrite the System boot files to the boot partiton or Windows 7 partition itself. If one fails, try the other.
You can use free Partition Wizard
bootable CD to Modify>Set to Active, then click on the Disk number to highlight it, from Disk tab select Rebuild MBR which can preclude the need to run the Repairs.