I am having a similar problem. I purchased LOMAC from Ubisoft via the link on the FC3 page. I downloaded and installed LOMAC, I can run LOMAC just fine. However, when I try to install the DCS Module (FC3_release_en_1.2.2.7122_19.exe), it tells me that Lock On: Modern Air Combat must be installed.
Now, the problem may be that I am having difficulty registering LOMAC, because the registration program built into the game keeps telling me that it can't find FMV4Installer.msi, but since LOMAC itself is installed and is playing and fully functional, I don't think that's the problem.
I can run DCS: World and was able to install the update for A-10C. I can try downloading and installing the update for CA as well, but I suspect that should work too. Now, when I run DCS: World it says that there's an update available and do I want to download it, but I thought it made more sense to install the modules (since they're all the same version) and then do the update, otherwise the downloaded modules and DCS: World version would be different.
Sad part? I'm a computer programmer, I should know this stuff. I swear, staring at code all day must be rotting my brain or something. Since other people can presumably get this to work, I must be doing something wrong.
Edited to add: I ran the update for DCS: World, it barely took any time to download, so must have been minor. Still getting the same message when I try to run the FC3 module installer.