I've noticed in a few older games, notably the Doom series and Wolf 3D (those are the only two I've tried it in so far) that if I press ctrl and alt at the same time my screen orientation and resolution are changed on my desktop. Anyone else encountered this problem?

Some of the GPU control panels do have the ctrl-alt-arrow as an orientation shortcut. Take a look at said settings, since it should have nothing to do with DOSBox.

Yup. Thanks, that's it. I'll have to mess with my setting then.