Version 3.6.0
I am using the latest version of software with the latest model of AppleTV A2843. I am using the beta version of tvOS (18.3 [22K557]) but this issue has remained over many versions of tvOS over the last several months.
I play movies or tv show episodes from a NAS. They could be .mkv, .avi, or mp4, the format does not matter. Sometimes the formats are random and sometimes they are the same. The AppleTV is hardwired to the network. For speakers I am using two HomePod minis. They are also running beta version 18.3 922K557. Again, I do not think the software has any bearing on this issue as it has remained over many versions and is due to a setting within VLC.
When I am playing a video, it loads correctly, the audio and video are sync'd fine. When the file ends and it progresses to the next file in the folder it will add 1000 ms of audio delay. This happens consistently. If I go into the settings and reset the delay back to 0 the issue is corrected. Once the file is over, the next one will add the delay again. I do not see anything in the settings to address this issue. I don't know what benefit this would provide or if this is some kind of bug in the software.