Tuning line width and flow compensation in Cura I'm currently in the process of fine-tuning my cheap CTC i3 clone. I'm using Cura 3.1 for slicing.

After calibrating the extruder steps, I wanted to optimize the line width and flow compensation parameters. I am using a 0.4 mm nozzle and therefore set the line width parameter to 0.4 mm in Cura. I then printed a cube with 0% infill, 1 wall line and no top layers (basically an open cube with 4 bottom layers). The wall width I measured on the printed result is 0.52 mm. To correct for the difference I set the flow compensation to 80% and repeated the print. The wall width I got from this was 0.45 mm, which is much better than before. There is only one problem: the parallel lines in the four bottom layers do not touch, so the print is not watertight. Up to now I assumed that Cura would calculate the distance between the lines from the line width setting. So with 0.45 mm lines and line width set to 0.4 mm there should even be some overlap.

Why am I seeing this effect? Am I getting something fundamentally wrong here?
That is very bizarre.  Since GCODE describe each movement of the printing head (so, the printer does not get to decide anything in terms of printing strategy, it just executes), I can only see three possibilities that would explain what's going on.

The print is being scaled up at printer level.  This could for example be due to your firmware having your steppers improperly calibrated and moving them too much for a given unit of measure (say you say 1mm, they move 1.5mm instead).  This is easy to check: if this is the case, your cube will be scaled up (so - using the example above - if your cube is 10x10x10 it will come out 15x15x15).

You are printing with a raft.  Then there is no problem with your set-up, the first layer(s) of a raft are not solid, but intentionally "grated".  Check your settings to verify.

Cura is producing the "wrong" gcode.  This could be really wrong (as in "you found a bug", in which case you should report it on their github), or just look wrong (as in "you found a weird combination of setting producing that gcode", in which case you should reset the settings to their default and see the problem disappear).  Either way, if the gcode is "wrong", you should notice the gaps in the gcode preview mode in Cura.