I use sqlite databases in Qgis, but need a more fully featured gui to fix index problems which Qgis tends to accumulate and have been advised to use this software. The problem is, it won't open any of my databases reporting each time a malformed database schema on a syntax error. I should emphasise that all of the databases I've experienced this error with are working perfectly well in Qgis, I can load them, run queries, add, edit and remove data and features, all without a problem.

So, if it is possible to load and work with such databases (which Qgis shows it clearly is) could you please allow them to be opened in spatialite-gui so that the errors can be fixed?

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.