In full screen the game doesn't register small mouse movements making it almost unplayable. In window mode it works well though.

Does anyone have a guess why my mouse doesn't work normally in full screen and how could I fix it (other than playing in window mode)?

It's Logitech G9 Laser mouse. I'm using Windows 7 32 bit.

First of all: make sure you have set either OpenGL, Direct3D or DDraw as Graphic mode in the "Graphic mode setup" tool that GOG provides, else your processor has to do the scaling and that may tax your processor unnecessarily.

If that does not help try editing "dosboxROTH.conf", find the line "sensitivity=100" and try higher or lower values and test the results.

Edit: Also take a look at this thread, seems to be a similar problem:
http://www.gog.com/en/forum/general/mouse_problems_specifically_xiii_and_arx_fatalis

Thanks, the OpenGL did the trick.