Extremely Slow boot time on windows only, ubuntu unaffected

Hi all,
So I have an old Gateway desktop that nobody uses anymore so i thought i would install ubuntu on it. I wiped the hard drive and installed the latest ubuntu and all was fine and dandy. But i got tired of the lack of support linux has for many Windows-only programs so i decided to switch back. I made a bootable flash drive with windows 7 home premium x64 on it, and went through the install process. Everything worked fine, but one day the computer took 15 minutes to boot up (it was hanging on the "welcome" screen) and was INCREDIBLY slow to use once it booted. Of course I tried to reboot and i even rebooted into safe mode but the result was the same. Since i didnt really have anything important on the computer i just decided to wipe it again and reinstall windows. I went through the install process, but when i got to the screen that says "windows setup is preparing your computer for first use" it hangs and ive given it hours but it does not change. I thought maybe my hard drive might have gone kaputz, but when i wiped the drive YET AGAIN and installed ubuntu, it ran normally with my normal boot time of around 45 seconds or so. Is it a problem with windows only then? It doesnt seem to be the hard drive but does anyone have some insight as to why this is happening? I really want to get windows back on there and have it usuable so any help that you can give would be great. I apologize if i am not clear on something I am somewhat experienced with OS's but I have a ways to go.
Thanks!
BlindManPew

Ok so I attempted to install Windows again and this time I continued to wait and I got to the desktop finally. But now the desktop is very unresponsive. It took maybe 20 seconds for the start menu to open when I clicked on it, and control panel seems to be taking over a minute to open. I will have a look at the bios and see if anything is amiss but I really am lost.

Perhaps unlikely but can you check that disk with Partition Wizard free - surface test? I wonder if Windows uses some bad portion of HDD that Ubuntu doesn't?

The computer is soooo extremely slow that I'm not sure i can even get it to install but ill give a shot thanks

HOORAY! IT IS FIXED!
So I just opened up the computer and pulled the motherboard battery out for 30 seconds and then replaced it.
I don't know if that means that the cpu was in compatibility mode (I read something about that somewhere) or if there were just some weird settings in the bios.
Thank you to GokAy for replying though it seems as if my hard drive is ok. I might run the test just in case.
Thanks!