[propbeanie]

This happens in SH3, and 4, probably also 5, and it is due to the player shelling-out to Windows, either purposefully to do web browsing, use targeting tools, or whatever. But it can also happen due to (especially) Windows 10 and little apps running in the background that "pop-up" for notifications. When the computer shells-out to Windows, the game gets interrupted, and then "loses its place" in the grand scheme of Windows and buffers. The game is an old DirectX v9.0c, single-core game written to the Windows XP paradigm. You might also notice graphic anomalies, such as a pillar of smoke following your submerged sub, or sound issues, such as missing voices or sound effects, after shelling happens. The best thing to do is not shell-out, and use your fone (tablet, 2nd computer, etc), if you need something outside the game. Saving the game, then exiting completely, then fire the game back up and Load the Save is the only "fix" once you encounter the issue. No patch or mod can fix that.