Helping people with computers... one answer at a time.
After making changes using msconfig it restarts on your next boot and presents what appears to be an error message. It's not. I'll look at what it is.
There are items showing up on msconfig's start-up list that I want to disable. But, when I do so, and re-boot, I get the "System Configuration Utility" error windows that seem to want me to go back to starting what Windows wants me to start, not what I want to start.
How do I disable entries on msconfig and make Windows happy with my decision?
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Actually, Windows is quite happy.
The problem is simply that, like so many of us, it's having a hard time expressing itself clearly.
I'll try to interpret.
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The scenario that you're in looks like this: you've run the msconfig utility and made a change to one or more of the items in the "Start Up" tab. Perhaps you've unchecked a few items that were running at start up that weren't necessary.
When you press OK, msconfig then asks if you want to reboot, which you do.
After the machine reboots and you login, you're presented with this message:

That fairly daunting message is not an error.
Instead, it's msconfig trying to be helpful.
What it's saying is simply this (I'm not trying to be condescending in my choice of words here - it's a complex message, and I do want to present the concepts simply):
I (msconfig) see you used me to make changes prior to the last reboot.
Because of that I now automatically run when you log in.
I do that just in case the changes you made caused some kind of a problem.
You can undo those changes by selecting "Normal Startup Mode" after you press the OK button below.
If everything looks OK check this box and I won't bother you again.
The magic of course is that last item. All you need to do is check the box that says "Don't show this message or launch the System Configuration Utility when Windows starts", and click OK.
It won't bother you again. At least, not until the next time you make a change.
If you don't check that box, this message will reappear after every reboot until you do.
What I personally find most fascinating is that this message no longer seems to appear in Windows 7. (Not sure about Vista, I didn't test it.) Apparently the confusion you're feeling was common enough to cause them to rethink the whole idea.
Article C4340 - June 11, 2010
The biggest problem for me is in a Corporate environment where users don't have admin rights. I log into MSConfig with other privileges while another user is logged on and make my changes. The user then reboots, logs in again (usually the next morning), checks the box and clicks OK, but the error keeps coming back because you need admin rights to get rid of it for good.
Posted by: Chris at June 16, 2010 9:53 AMmany folks use C Cleaner for controlling cleanup of the system and to handle registry cleanup and don't realize that under Tools there is an option to control startups and the cryptic msconfig message does not appear. To help with startups, use www.bleepingcomputer.com/startups
Posted by: Murray White at June 16, 2010 10:05 PMChecking the box does not cause the message to quit appearing. It appears EVERY TIME I reboot. I wanna just chuck the laptop out the window. I am running Winders 7 64bit, and I've searched long, hard, far and wide for a solution to this annoying popup.
Posted by: DJGray at September 20, 2010 5:59 PMDJgrey....... have no clue as to why that would happen to you. One of the first things I do after a re-install is to head there and uncheck most of the startup's haha. Have you ran sfc/scannow to look for/repair corrupted files?
Posted by: indianacarnie at January 6, 2011 11:49 AMThis advice no longer applies as in Vista it pops up a small toaster message in the status bar - and even when you close it, it keeps popping up again at some interval. It's hard to understand, at this point, why Vista even bothers to allow you to block something when doing so causes so much annoyance that it has to be undone. Im doing this for a "mum/dad" pC - the popup message blocks what they're doing by hovering over all other programs. Unbelievably annoying & confusing & worrying to them. Im blocking Windows Installer Module because it wouldnt stop using 50% CPU for 24hrs a day.
Posted by: FurryMoses at December 23, 2011 4:23 PM