I am pretty sure Cakewalk FX2 are not VST plug-ins. They are DX plug-ins so the VST scan process does not matter. You need to make sure to run the installer as administrator and it may be necessary to run MC6 as administrator to use the plug-ins. Since they are DX plug-ins they will show up at the top of the plug-in list.
I do not have amplitube 3 but I am guessing you are working with the free Custom Shop version. Make sure that you have registered it and that it works correctly in stand alone mode. Then make sure that MC6 knows where the 32bit amplitube 3 VST plug-in is installed by adding the location to the VST scan path. The run the VST scanner.