Thanks a lot for your feedback 
Not only is the lightening a problem the shaking screen is worse!
I see... we've added an option to disable thunder light effects with the latest hotfix (this will also turn off the shaking)
To do that, go to the settings menu to "Miscellaneous" and scroll down. This option is almost found at the bottom of the miscs settings.
But I imagine my bay may be freshwater ...? I guess I will see.
It depends on the connection to the sea. If it's just a narrow connection, it's often freshwater. If it has a lot of contact with the sea, it's typically saltwater 
Oh, idk if this is a bug, but chickens are laying eggs while the game is paused! Just confirmed it.
Oh, was the game really paused (i.e. ESC was pressed to bring up the menu)? Or did you just alt-tab to the desktop? The latter basically only stops the rendering process (for energy-saving reasons), but most calculations still go on in the background 
I just found a bug though. I can't eat cookies. The animation and sound work, but the cookie is never eaten, and health is not restored.
That was unfortunately indeed a bug, but it should be fixed with the new hotfix 
I have noticed lightning in a clear sky in an arid biome. I'm assuming this is stormy weather in temperate biomes. That can be fixed in a hotfix or than need more work to implement local weather ?
Oh, thanks for letting me know! It's interesting to know that this could apparently happen IRL CursedXistence , but it was not intended
I will change that with one of the next hotfixes!
But i noticed, what i think is a bug. I was inside, door closed, a thunderstorm was going on with heavy rain. Impressive! But my avatar did make sounds and started to shiver indicating i had it cold ? The perceived temperature was 30 degrees. I think when it's a thunderstorm the system doesn't notice that i'm inside ? The behavior was typical for if i was outside in the storm.
Hmm... was it maybe just the brief camera shake that occurs if a lighting strikes nearby?
If it's temperate related, the game will always show the blue temperature icon in the lower right corner of the screen (but that seems to be unlikely if the perceived temperature was 30°) 