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
