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
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".
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!