version 1.2.1 was released in 2009, and is nowadays incredibly obsolete.
it's not at all surprising to discover that it's completely unable to
correctly access database files created by modern versions of QGIS surely
based on recent versions of both libsqlite3 and libspatialie.

please update your spatialite_gui to a more recent version and you'll
soon discover that all your troubles will be immediately resolved.