4GB limit, chunk download, what to use to demux and remux?

[MS]

I'm trying to download the Fencing from Tuesday, Men's Individual Foil, 
using the Olympics 'live' feeds in HD 1280x720. Urls below, 6 hour heats 
session, and 3 hours semis/final/ceremony session:

http://www.bbc.co.uk/sport/olympics/2012/live-video/p00w2xsr
http://www.bbc.co.uk/sport/olympics/2012/live-video/p00w2y8v

Like others I've run into the 4GB limit. My first attempt was on an EXT4 
file system (Linux, Ubuntu), after get-iplayer stopped downloading I 
checked the file size, it was 3.99 GB. I then tried again, by chance 
saving to an older drive, EXT3, the same exact thing happened.

So I'm trying the chunk download solution, for my 9 hours of fencing, 
using --start and --stop.

The first chunk of each session works fine, no --start just a --stop, it 
stops correctly, and converts to MP4. The subsequent chunks, when both a 
start and stop time are specified, all seem to stop a little bit early 
with errors, initially a exit code 2, then a mass of exit code 1.

INFO: Command exit code 2 (raw code = 512)
INFO: Command exit code 1 (raw code = 256)

BUT they only stop a little bit short of my specified stop point, and 
the video plays in VLC perfectly well but with a mucked up timecode.

By adjusting my start and stop points I am confident I'll be able to get 
the whole of the 1st (6 hour) session, I already have the whole of the 
2nd (3 hour) session.

So how do I fix the downloaded chunks? What Linux software do I use to 
demux my 1st chunk .mp4 file and subsequent chunks .mp4.flv files? And 
what software do I use to remux them together preferably allowing a 
little editing to get rid of the 5 min overlaps I've used for the 
chunks, and fixing the timecode? (If timecode the right expression for 
the time displayed when playing the video?)

I'm not sure how to do this, I had a little experience with 
mplayer/mencoder last year, but nothing this advanced.

Any advice would be really appreciated. Many thanks,

Matt