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Configuration file been ignored when launch from command prompt

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I have a quite simple application which compiled target .net 2.0.  It works fine on both machines installed .net 2.0 or .net 4.0 as long as I attatch a configuration file to specify the application to support 4.0 or above. Here's reference:

How to: Configure an App to Support .NET Framework 4 or 4.5

However the problem is when I wanna do some automation via batch file or launch it from a command prompt on a machine which only installs 4.0, the configuration file seems to been ignored, and a window pops up instead prompt me to install .net 3.5

It looks like the configuration file is load differently from default way, or even been totally ignored. But I could't find any related info to confirm my speculation, neither any workaroud.


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