If a custom plug-in setting, an EXS instrument, or a channel strip setting does not show up in its respective pop-up menu, check to see if you may have saved the affected item under a name that begins with a minus sign (-), such as "-3 dB." Logic excludes files with names that begin with a minus sign from its pop-up menus.
If this is the case, rename the affected file to resolve the issue. You will need to locate the file in its appropriate subfolder in ~/Library/Application Support/Logic/Plug-In Settings/.