I found a Steam Community Discussion relating how several people using multimonitor configurations are only able to select the maximum native resolution of their primary monitor. I use a dual-monitor multimonitor setup and do not experience this issue. However, they're discussing the Steam version, not the version I use, which is the DRM-Free version offered for free as a promotion on the Humble Store (which, BTW, is only available for download until September 14; check your Humble Store library for more info).
Anyone with the promotional free release able to replicate the issue reported on Steam?