W98SE Startup stop

At home I am running Windows 98SE on an AMD 900 system, in the last type some changes have been done because security and Windows updates and …
My problem is:
during the setup and after AUTOEXEC.BAT my system does stop for around 60 sec, no activities and it did not use to do it before
My question:
Where can I change it and why does it happens??
Regards