We might not be able to figure out a solution for this, sadly. Ossuary is made in Adobe AIR, which is an old and weird technology that makes diagnosing this sort of thing hard. My guess is that the game somehow incorrectly thinks that your monitor is smaller than it is, and is resizing/scaling itself smaller to fit. Are you using a high-DPI monitor, or doing something else interesting display-wise? If so, there may be compatibility settings that could help.
I can understand that playing the game in a little box isn't a good way to experience it, and I'm sorry if we're unable to come up with a fix. If you find it an acceptable workaround, you can use Windows's Magnifier utility to zoom in on the game, but obviously that's not ideal.