(...) That uneven movement annoys the hell out of me.
I have not run into the issue myself, but this may be related to the option to keep the correct aspect ratio in DOSBox. The latest GOG version of Synd still doesn't have that option turned on by default (it really should), so you might want to test it if you play now and still have issues. You can change that option in the "Advanced Settings" tab of the "DOSBox Configuration" program included with the game.
If that still does not solve it, using some additional software (like ZFR suggested with AutoHotKey) is the only way to fix it, since the latest official release of DOSBox does not have a separate sensitivity setting for X and Y mouse axis, and Synd includes an even older one. You could use the configuration software of your mouse, if you own a gamer mouse
of some kind.
The latest DOSBox SVN builds do have the possibility of setting different sensitivities (and even inverting the axis if needed for some game), but that is probably a more "involved" solution.