I have a mp4 file which when I cut a clip from using FFMpeg with "avoid_negative_ts make_non_negative" argument has a slight freeze near the beginning when played in VLC media player, the clip plays properly when I don't use this optional argument. When I cut out the same clip using Avidemux, I get the freeze which makes me wonder whether it does alter timestamps?
All timestamps in Avidemux are non-negative by design. Regarding the problematic file, if the issue persists with the latest Avidemux nightly build (https://avidemux.org/nightly/), could you please provide it as a sample (of course, only if it is innocuous enough) via WeTransfer, Mega, Dropbox or Google Drive and provide also precise editing steps.
Some elaboration, because I completely forgot to mention that I was doing cutting without reencoding, only copying streams. It's not about just a single problematic file, it has happened many times and also seems to be unique to VLC media player. I was first cutting clips using LosslessCut program and realized that many of them have a slight freeze near the beginning when played in VLC, LosslessCut has enabled by default option "Shift timestamps (avoid_negative_ts) - Make Zero", when I disabled this option, the resulting clips played properly in VLC. I also learned to use FFMpeg myself as LosslessCut is a GUI built to use it, and learned that it's about this "avoid_negative_ts" optional command line argument, and I can see the same thing happening when cutting the clips out with FFMpeg, when I turn it on, I get a clip with slight freeze in VLC, without it, I get good clips. Now I also tried with Avidemux and some clips have the exact same problem I had with LosslessCut initially, which is why I ask whether it does shift timestamps similarly to how LosslessCut does by default.
Did you try the latest nightly? The release is obviously missing bugfixes from the last half of a year, so it is almost entirely pointless to waste time testing with the release.
And if the issue persists with the nightly, nothing can be done without a sample video which allows to reproduce the problem.