2.6 not responding
Probably need a video expert to comment on this (thats not me!).
However I'll try and hope others will refine and correct the nooby response.
1) thats a big transport stream file.
2) DVB derived? - means lots of timing information for maintaining sync between streams inside the .ts (then add consideration of 1).
3) DVB also means lots of timing information for resyncing after lost packets.
4) If it is an .m2ts then probably it came from a camera, and this has extra timing info (help with editing).
5) Avidemux 2.6.x wants all this container timing metadata because it can be an editor (so has to read and interpret the whole thing).
6) Handbrake is not an editor so can transcode frames on the fly (no need to read and interpret the timing of the whole thing).
Maybe try and remux first to a better container like MKV might help?
You don't clarify which 2.6.x version you use.
Try the latest "nightly" version.
Or try 32bit version (sometimes more stable than 64bit version).