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I have made few changes and needed to reset IIS. But most times when i do it using STSADM it stops application pools in iis, i have to restart them manually.

I dont want to do it manually all the times, any quick solution

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The application pools should restart on an iisreset, but they do run outside of iis (in COM+) for reliability. This mean they may may not come back if the application is misbehaving, but IIS and the other apps will(should) come back. So yes, This is "normal".

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have you tried IISreset /NOFORCE ?

Performing a IISreset is ment to stop the app pool but then restart it.. Somethimes it gets moody and doesnt restart!

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