Boot up getting ridiculous

I believe the cause was a prog from Giveawayoftheday.com a photo touch up prog, which refused to work in Windows 8 64bit. I rebooted trying to get it to work.
It took between 10 and 20 minutes.
Horrified, i removed the program, and rebooted. No better.
I reinstalled windows, after trying different things including "repair my computer" which if anything made it worse.
It comes on with the Asus screen (the mobo) and before it was 2 seconds, now its 2-3 MINUTES. Then beeps, goes onto the same Asus - as before, but that lasted say 3-4 seconds, now it's 5 minutes plus. Then onto Windows screen which takes a further 5-10 PLUS minutes whereas before it was seconds.
I reinstalled Windows as I say. Maybe it's got SLIGHTLY faster, but not the 20 seconds maximum it was before. What can I do ?

Oh one other thing. I noticed also that if I leave the PC for a while, I have to reboot the damn thing instead of just moving mouse.
And with the reboot lasting so long....

Laptop or Desktop?

Did you reset the BIOS to factory defaults?

Did you remove all USB devices (including printers) and remove all disks from all drives?

Did you reinstall Windows from software on the hard drive (factory restore) or from a Windows CD/DVD?

Did you uninstall the program from Control Panel "Program and Features"? You may not have gotten a complete uninstall. Re-install the program and uninstall it with Revo---http://www.revouninstaller.com/

Did you run Virus and Malware scans?