We got the package stored in MSDB to execute via ASP.NET page when running page from Visual Studio server on a remote admin machine, but when the page was deployed to the Intranet, the package would fail.
I don't understand what you mean by deploy to intranet because the Agent it is automation tool so it needs to be in MSDB and not file system because if you deploy it to file system then you need to take care of Asp.net file permission and could escalate to Asp.net reflection permissions. That is the reason you use the Agent subsystem for all Asp.net execution.
Kind regards,
Gift Peddie