A persistent timing issue sounds to me like the hook isn't tightened correctly when timed. Not having everything tightened up well means the hook can slip again causing problems. Have you had some serious thread wads in the bobbin area? That is about all that should be able to mess up timing. It actually is remarkably easy to adjust timing on a machine; I have done it on my multineedle embroidery machine when installing a new bobbin case.
Hope you get satisfaction from your dealer and/or Janome.
Pam