Some of the Jubilee line is quite new - unfortunately a lot of the work is having to be done on the new part, because the tfl powers that be just didn't forsee it being used as much as it is today. Currently, the way the track and signals are organised, only one train at a time can go through the long stretch of tunnel between Canada Water and Canary Wharf. This leads to a huge backlog of trains at peak times, which is why gaps between trains are longer on the Jubilee line than for other lines, and why many trains end up terminating before their advertised destination, so they don't add to waiting times to go through that particular portion of tunnel.
Much of this is due to lack of forward planning when the line was extended. After the extension, cheap housing at the eastern end of the Jubilee line suddenly became feasible (and far far more affordable than most other parts of London in zone 3) for people working in the centre of London, and demand increased far more than had been planned for.
A large part of the works going on is to change the track and signalling in that one stretch of tunnel - which will increase the number of trains per hour at peak times by around 50% (and by around a third when averaged out over the day). This will be an absolute godsend to those of us living at the east end of the line (especially those who have to get to the other side of London for work), but it has been a complete bloody nightmare for those who have to work weekends in the meantime while they upgrade the line.
The worst thing is that sometimes they don't co-ordinate well and take out both the Jubilee line and DLR in east London at the same time, and the replacement bus takes ages because there is no direct route by road, it has to go through the Blackwall tunnel - absolute bloody nightmare - I just wish they would co-ordinate to take each line out on alternate weekends, rather than leaving us with absolutely NO rail based public transport every other weekend!