If you are SURE,
that the files which correspond to the disabled msconfig-entries are gone, then reenable their entries in msconfig and make a new hJT-Log (maybe after reboot)
and fix them there
(it should say now “no file” in the line)

or do a manual search in registry, or use some regCleaner

P.S.:
Imho HJT doesn’t list startup-entries that are disabled via MSCONFIG, as they are inactive… (that’s why you don’t see them in HJT)