I haven't been able to reproduce the problem in the preferences screen with coloroing so suspect that this issue has already been addressed and will be available in the next Atelier refresh (coincides with the next 2016.2 field test beta posting).

The DLTK indexing initialization error is new and has been raised as an issue for our development team

Ref: Server view and copy of routines. There are server filters available for System and Generated files but they do not seem to be honored at the moment. I'll raise an issue for that to be addressed.

Thanks for the reports

Yes, the HTML is an example of an 'embedded' parser. Much work has been done in this area but there is still more to do. The good news is that we have developers working on that now.  We understand that the Syntax Coloroing is really important, please be assured that we are giving it all we've got to resolve these issues.