Audio cuts out at 48:20 in MP4 and MOV movies

[GammaBoost]

I converted some movies to MOV files I can play on my Old 3DS using Avidemux, and for some reason the audio completely cuts out at 48 minutes and 20 seconds. I remuxed the files to MP4 and I get the same results, but if I instead remux to an MKV container then there isn't any issue. I haven't tested enough to see whether the results change with any other audio bitrates or codecs, but it didn't occur when I played a long .m4a audio file by itself.

The video compression settings I had this issue with:
MOV or MP4 container, encoded with Avidemux 2.8.2 nightly
MPEG-4 ASP video (xvid4) at 400x224 24fps
AAC 2ch Stereo audio at 160kbps (FDK)