Hi,
in the old StaxRip version (1.0 and following) all settings (like p.e. desired number of output pixels in video) were global. Since version 1.1, the following happens if those settings are changed when creating a new project and settings them (p.e. disabling subtitle extraction): nothing - the settings apply to the current project but not to the projects created thereafter.
If course the settings are saved if you modify them in the corresponding template, but that's in my opinion a little bit more complicated than necessary. Is it possible to change this behaviour so that settings can be set globally in current projects without having to modify the corresponding templates, like it was in the old version?
Dust Signs
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I don't think there are fundamental problems with the project/template/job concept, bugs are always possible of course. Everything in the project options dialog for instance are project/template/job settings and not global settings like the things in the settings dialog, the profiles/presets, event commands etc. If you want project options to persist you have to change every template. Maybe you are relative new to StaxRip and don't have the best understanding for project/template/jobs/batch/profiles/presets related features.