Fusl
When minimizing the application window, the registry keys
HKCU\SOFTWARE\VRChat\VRChat\Screenmanager Window Position X_h4088080503
and
HKCU\SOFTWARE\VRChat\VRChat\Screenmanager Window Position Y_h4088080502
are being updated with values that appear to be offset by around 4294967295 which causes the application to spawn its main window at 0,0 on the next startup.
Reproduction steps for normal behavior:
  1. Start VRChat (through Steam)
  2. Ensure VRChat is in windowed mode
  3. Resize the VRChat window to something smaller than full screen (for example half or quarter of your monitor resolution)
  4. Move the VRChat window to the lower right corner of any monitor (preferably to a monitor that's not top-left on a multi-monitor setup)
  5. Close VRChat normally
  6. Re-open VRChat (through Steam)
  7. The application window spawns at the position it was last closed at
Reproduction steps for abnormal behavior:
  1. Repeat steps 1-4 from above
  2. Minimize VRChat
  3. Close VRChat (either through Steam or through right-clicking the taskbar icon)
  4. Re-open VRChat (through Steam)
  5. The application window spawns at position 0,0 on the most top-left monitor