The logs look fine. Is your hardware otherwise OK, i.e. can you run memtest without any errors for hours? Maybe there are encoding errors which go unnoticed on more error resilient software decoders compared to your hardware decoder? I'd also say that you may want to look for bitrate spikes, but if your original 720p files already work fine, it's unlikely to be the source of the problem.
If you cannot find the error, you might want to test out
HandBrake. It can burn in ASS subs and encode to mkv and mp4, all in one step. It only supports AC3 passthrough though, but that way you may be able to see if mkvmerge is at fault.
Just to be sure: you ARE remuxing your files with mkvmerge before putting them onto your phone, right? Because x264's mkv output has no index, which prevents proper seeking.