Don't worry about it. I know where you guys are coming from, and I'd be just as frustrated.
Here's what happened, as best as we understand it:
Nvidia releases some new drivers which up the performance for most games, ours included. Yay!
We released an update to Pirates which increased the perfomance pretty dramatically. Yay!
Combining the two, we're hitting frame rates that we'd never hit before. Yay!
Once we hit a certain frame rate, the flickering starts appearing. Boo!
We actually had a similar problem a while back, when the game would run faster than the monitor refresh, the wake would start flickering. We assumed it was a problem on our side, and attacked it that way, but after a great deal of investigation, found that it was on the driver side. How long it's been there we don't know. It could have been created by the new driver, or it could have been the speed improvement of the Nvidia driver and our performance improvements hitting at the same time. Regardless, it's there now, and Nvidia is investigating it. Until they can find the root cause, the only thing we can do to remove the problem is to slow the maximum frame rate down to what it was before both patches came out.
Of course, that's not a good solution if you're not having the problem at all, and want maximum performance. So we made it a variable that you can adjust. To get at it, put the attached ini file in C:\Program Files\Flying Lab Software\Pirates of the Burning Sea. If you already have a file with the same name there, copy the contents of this ini file to the other file. The sole variable is MaxFrameRate, which lets you throttle how many FPS you're getting. It's set to a hundred in the ini file, and 40 in the patch (that solved it for all of the machines in the office).
Obviously, none of this is supposed to be a real solution, it's a temporary one to allow you to continue using the faster Nvidia drivers for your other games and not have the flashing with Pirates. As soon as Nvidia finds the problem, we'll let you know what it is and when you can expect the real fix.