Sometimes, if two plug-ins have similar names, Cubase assumes that the plug-in files are duplicates and only scans one of them, thus leaving the other one out.
The way to get your automap plug-in to appear is to remove the original .dll file from your VST folder:
PC - (C:/Program files/Steinberg/VST plug-ins)
Mac - (Mac HD > Library > Audio > Plug-Ins > VST)
Now, open cubase so that it scans for the Automap.dll file, then quit Cubase and put the original .dll back into the VST folder. Now Cubase should only see the Automap version of the plug-in, but the original plug-in is still in its correct folder.