More POSSIBLE solutions, BUT yet unconfirmed:
Try to fix it by enabling GPU Scaling/Maintaining Aspect Ratio in the driver menu of your GFX card.
Also unconfirmed: open Main CFG file in My Documents with Notepad change Synchronized=No to Synchronized=Yes
Better yet, make sure "disable fullscreen optimizations" is unchecked in the compatibility tab.
CHECK ON: Override high DPI scaling behaviour. make sure that the checkbox for "Override high DPI scaling behavior. Scaling performed by: Application" is checked.
Try deactivating the second monitor. the active monitor has to be monitor 1
Possible solution, yet unconfirmed: Your d3d9.dll file may be outdated. Make a backup of it first!
Step 1 - Navigate to C:\Windows\SysWOW64
Step 2 - locate and copy the d3d9.dll file
Step 3 - Navigate to your SH3 folder
Step 4 - Paste and replace the d3d9.dll file
Run dxdiag.exe, it shows the version.