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I am having similar issues with subtitles in Batch Mode (Automated - Folder Selection), I have the batch setting checked on to render subtitles. So it is de-muxing the PGS subs correctly from my MKV files no problem but the MP4 created are not getting the subtitles rendered into the finished file. It works fine for me if I manually convert a video and select the subs to render in AviSynth settings. Am I doing something wrong? Any input would be appreciated. I am not sure how to post an example of this issue.
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