Security error after install web site with cmd file

[JJJ]

I web site is installed on v1 with a setup (msi).
I upgrade the web site with a file .cmd

After this operation : SecurityException /
AspNetHostingPermission

If i execute manually the "aspnet_regiis -i"
-> the web site is OK

If i insert in thge cmd file the line "aspnet_regiis -i"
-> the web site is not OK

Can you help me ?