There are two problems that can appear similar.
The first is that for some of us, don't know which or why, ModBuddy does not copy the build to the installed mods folder, thus requiring that you copy it manually from the ModBuddy build directory. I'm guessing it's a settings issue, but I've never bothered looking into it.
The second is a refresh problem with the mod selection screen such that a copied mod doesn't show up in the list. The link provided by Iceco above can tell you all you want to know about that.