You can disable transitions, which save some time. The main level that is different (and far worse in my opinion) is Ice in the Hole, where the secrets are changed significantly. Or it could just be that your computer lags 0.5.1 slightly (it is quite a bit harder to run). Though theoretically 0.5.1 is quicker, generally they are both the same except 0.5.1 is harder for one level.
In 0.5.1 there is a door. In 0.4.0 there isn't. Not using the door is probably quicker unless you can frame perfectly jump.
In 0.4.0, there is a different secret involving going above everything pretty much for the whole level.
Vertical sync (vsync) basically stops the game running over 60fps or whatever set speed it should go at, which in some cases depends on refresh rate. For some people it is disabled, offering around a 1%-10% speed advantage depending on various factors. This doesn't make a difference to individual levels because it is done by in-game time, but it does affect full game/world speedruns because it is done in real time.
I was talking about Ice in the Hole for the secret, although vsync is for all levels.
You can (sometimes) turn off vsync by going into your config file and changing vsync #t to #f, which on Ubuntu is under .supertux2 in your home folder which is also a hidden folder. Although if that doesn't work you can try running vblank_mode=0 supertux2 in terminal. It varies between computers. IMO a better solution REALLY needs finding; faster computers have an unfair advantage anyway sometimes.
On the old Ice in the Hole, after the main secret you could do a jump that takes you above the entire level, making using the secret a lot easier and potentially quicker.
