Internet Explorer 6 has started to act weird. Home page is set to some page that I did not set as home page, during surf many pop up windows with advertisements are almost disabling surfing etc. At the same time I have noticed process nvctrl.exe in task manager. It is always there and it seems that this process starts with Windows. Is this a Trojan?
Yes it is. Fortunately it is a common hijacker and not some really harmful virus. To delete it download and install some good antivirus program, disable system restore (this will delete ALL system restore points), and perform a full system scan. Delete all detected files and you will be virus free. If antivirus complains that some files are in use and can not be deleted perform a scan in safe mode.