If you install Microsoft.VC90.CRT in more than one folder, you have to keep in mind that there may be more than one instance (*) of the runtime-library in memory if you embed a manifest in a DLL. This results in many problems. In example you cannot allocate memory in one instance and free this in a different one.
The best way is to create a dependency manifest in only one place (the executable). And build the extension DLL without a manifest. (/manifest:no as linker option).
(*) This behavior occurs only, if the runtime is not installed in WinSxS