Can you build projects in question manualy from the Project Manager?

>I have developed an build tool the uses a script language to build several projects and generate a installation package. The problem is that some of the project are failing to build do to a "File cannot be closed because outstanding references exist." I know it is referring to a open object, but I checked and there are no objects. I assume when the project is open and built that the class libraries are been cache somehow. If this correct, how do clear the cache?
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>If anyone have any other suggestion, please reply.