All I can offer is some help in determining what is not loading. If this is a dev server, it might be worth installing the appropriate sdk to use the Fusion Log Viewer . If this is not an option, you can enable assembly binding logging from the registry as follows:
Windows Registry Editor Version 5.00 [HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Fusion] "LogFailures"=dword:00000001 "LogPath"="c:\\bindFailureLogs\\"
just remember to turn it off when you are done, there is a performance limitation using assembly binding logging. Make sure the folder exists before you enter the registry key and restart the application's application pool to start registration. This will provide you with a detailed list of what the dll (or dependency, since it is not always obvious if it was dependent or the dll indicated in the error message) did not load and where did it try to load it.
Separating the applications that fix the problem indicates that there are several assembly dependencies for different versions, and since only one version of the assembly can be loaded into the application domain, some dependency is not executed. For managed assemblies, you can use assembly binding redirection , but I don't know what the unmanaged equivalent of this will be, if it even exists.
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