Each time I launched the game, it opened in a smaller window, and it kept shrinking every time. Currently it's 521×330 and stopped shrinking, but now it's completely unplayable.
I found a workaround of nuking the HKEY_CURRENT_USER\SOFTWARE\LemonJuice\Cypher key in the registry. Here's what was there before deletion:
[HKEY_CURRENT_USER\SOFTWARE\LemonJuice\Cypher]
"Screenmanager Stereo 3D_h1665754519"=dword:00000001
"Screenmanager Resolution Width Default_h680557497"=dword:00000500
"Screenmanager Resolution Height Default_h1380706816"=dword:000002d0
"Screenmanager Resolution Use Native Default_h1405981789"=dword:00000001
"Screenmanager Fullscreen mode Default_h401710285"=dword:00000003
"Screenmanager Resolution Width_h182942802"=dword:00000207
"Screenmanager Resolution Height_h2627697771"=dword:00000123
"Screenmanager Fullscreen mode_h3630240806"=dword:00000003
"Screenmanager Resolution Use Native_h1405027254"=dword:00000000
"unity.player_session_count_h922449978"=hex:31,37,00
"unity.player_sessionid_h1351336811"=hex:31,32,33,32,31,39,36,38,37,36,31,30,\
36,36,31,35,38,37,37,00
"UnitySelectMonitor_h17969598"=dword:00000000