The manifest file should be in the DLL built in VC. This VC DLL is the one that depends on the 'side-by-side' msvcr90.dll and so must have a manifest declaring this dependency. The CVI DLL has nothing to do with this issue and does not need any manifest - putting a manifest in the CVI DLL would not help. By default, VC automatically embed the manifest when it builds the DLL - so it should already be there in the VC DLL. You can see the manifest by opening the DLL in VC resource editor and looking in the RT_MANIFEST resource section.
I think the most likely cause of your problem is that the manifest in your VC DLL points to a different version/build of msvcr90 DLL - this could be because:
1) You are using a debug build. The VC redistributable only installs release build of msvc90.dll and this is different from the debug flavor of msvcr90.dll. Solution: use a release build of your VC DLL.
2) You have a newer msvcr90 DLL on your developement machine (may be because of some patch) but you are installing an older redistributable on the target machine. If so, try patching your target machine. I think 1 is more likely than 2.
