If you look in "msconfig-start up tab" and the path is the same, (C\I386) then it's clearly not necessary to run at start up. As you've seen, unchecking it and removing it from the "Processes" helps the situation. Unfortunately, I'm not sure why it's even there. I've checked quite a few machines and can find none with that Winnt.exe in the start up processes.
At this point, I would search for possible locations where the start up "call" is being initiated. It's your choice here as leaving it like it is should be just fine... BUT, If you can remove the start up call, the process should be removed from "msconfig" and should no longer be a problem. First, make sure to make a backup of the registry using the instructions below, then check the registry paths I list. Next, you'll need to go back and enable the process in "msconfig" and the "Processes" section. After doing so, restart the machine, then check in the following locations. If you find the key, then simply delete the specific key and the start up should no longer occur.:
IF YOU HAVE NEVER DONE THIS BEFORE, BE CAREFUL. First, make a backup of the Registry. Click on Start-Run. When the box opens type in "Regedit" (without the quotes). Click Ok. When the Registry Editor window opens, make sure all the registry keys are minimized by clicking on the - (minus signs) next to each one, then click "My Computer" in that window to highlight it. Next, Click on "File" in the upper left corner of the window, choose "Export". When the next window opens, make sure the "All" option is checked in the "Export Range" area in the lower left, be sure of the location where you are saving the file to (I usually save it to the desktop) and give the file a name like "Backup". Click "Save". You now have a backup registry that can be double clicked and will replace the new one you?re going to make, IF you make any deletions you don't like.
The registry paths below are good possibilities:
If you find and delete the "bad" registry entry regarding Winnt.exe, then click on the X in the upper left corner of the Registry Editor window, then restart the machine. If the problem is now gone, and everything is working correctly, then delete the "Backup.reg" file on your desktop. You don't want to accidently restore the registry.
Hope this helps.