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System Config Utility Problem/question

I was trying to reduce the number of processes that TSR at startup. I ran msconfig and unchecked a number of programs in the startup tab window. When I boot up now, however, I get a series of windows pop up that say I am doing a reduced start up, and nag me, finally ending up with the window that says I have to reboot for the changes to take effect, starting the cycle again.

I am running WinXP/home. I never had this type of problem with msconfig with Win98.

Questions: 1) how do you eliminate the pop window nags?
2) If you close or cancel the nags, have you stopped the processes?

Thanks in advance,

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