My first post like EBROWN would have been when was trusted paths introduced I think it was around 2013. You may not be seeing the error message about lisp not loading.
which year auto cad you are using?
after2012 you have to add them to the trust location in support file and make your save change to the work space selected
Like BIGAL my guess would be that they were not located in Trusted Folders. Were the lisp files in a different folder that the ones that loaded? You can add Trusted Folders on the Files tab in Options. If you don't want to have to include the full path when loading each lisp file add the folder to Support files in Options as well.
Using acaddoc.lsp as Lee Mac and others have suggested should at least give you an error message on the command history if not fix your problem. Startup Suite has always had problems like this, cant count the number of threads I've see involving "Startup Suite" over the years.
I'm not sure how the Startup Suite handles loading errors: it may be that the Startup Suite ceases to load subsequently program files if an error is encountered during loading.
