Cura does not use updated settings
If you change the settings in Cura, they are not used unless you restart Repetier. It's easy to test this if you change for example the bed/extruder temperature and check the generated g-code.
I have this problem on Repetier-Host versions 1.0.3 and 1.0.4 (I'm a new user, I did not use other versions) running on Windows 7.
This problem does not appear when using Slic3r