Starting with iOS 13, tvOS 13 and macOS Catalina subtitle handling was modified in standard applications. In some cases this has caused subtitles to show up for videos processed with iFlicks before version 3.4.
Luckily it is very easy to fix this behaviour. To do so, you can load the video file into iFlicks 3.4 and process the video with the Apple compatible preset. This is a very quick step that takes about a long as it takes to copy the video file and fixes the subtitle position.