There are a few variables you could remove to try and reduce it down to the simplest process. Try recording locally instead of NFS to rule out network corruption issues. Try doing a single recording with appending off and see if that is corrupt. Try stopping recording at onStreamDestroy to see if that makes a difference if you suspect so.
Play one of the MP4 files through Wowza using the vod app and check the access logs for anything of interest. This will probably give us the best clue as to what may be wrong. You could also analyse the corrupt files using the ffmpeg tool ffprobe
fprobe -show_streams your.mp4