Computer boot fine, but then gets really slow

Need help. Computer boot up fine, but while loading the start-up program (all have been removed in msconfig) its get really slow about five minutes to open any thing(task manger , control panel or anything you want to open. Its run fine in safe mode. Went into safe made run virus scan, search and destroyed, malwarebytes, and two or three register cleaner,defrag hard drive and register. I also done a repair of windows. None of this has done any good. I put another set of windows on this hard drive without format and this is working fine. Just want to try to get the other OS working as I have some programs that I cannot reload. Thanks Jerry

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