I don't see where that would be affecting you, if you don't have salmonella (and you would know it if you had it!). I almost always eat my eggs with the yolks a little runny.

If you've done scrambled for years it could be psychosomatic. I get weird about eggs and meat sometimes. If I think I taste something "off" I will end up feeling sick (even if nobody else notices anything). We've lived through a lot of egg-freakouts in our time - cholesterol, salmonella, low-fat craze. How recently did you switch? And are you cooking them in more fat by and chance? When I started upping my fat, I felt kinda woozy in the mornings.

Time to experiment. Don't eat eggs for a week or two and then going forward slowly incorporate an element of the egg back in. Example: Whites. Omelet. Poached soft. Whatever preparation you like and see what you react to. There are people who can't tolerate the yolks, some can't tolerate the whites.

If you want to eat eggs this is what I would do.

N=1 rules.

Note: I started to have a weird reaction such as spots and puffy-ness and it was the quantity of eggs I had each week. After N=1'ing my face off found that I can have 6 a week without issue. Any more I react. Good luck!

Way late to this but wanted to chime in since I have a similar issue with runny yolks- I feel just kind of off (flu-like spacey rather than any GI issues) after eating eggs that are less than completely cooked through. Poached eggs and even scrambled to less than dry bring it on, hard boiled or over-hard do not. We figured this out months ago and I haven't had an issue since adjusting the breakfast cooking routine then tonight we decided to make eggnog from scratch using raw eggs, and I am having the same feeling. I read about the egg white histamine thing so I took a Benadryl and am waiting to see if it clears up. It seems to be helping but it's hard to say for sure (felt much better right about the time a pill would kick in so there's correlation at least...).

The next time you have the feeling, try taking an antihistamine- runny yolks may just mean that the whites aren't cooked through either and are causing the reaction.

My very first keto experience left me sick of eggs. I was going for about 6 per day, and no matter how i cook'em, they made me feel like crap. Stopped for a month, re-introduced them and ever since is a stapple. For some reason, it was psychosomathic, which kind of is my bet on your situoation. Remove them for a period of time, and reintroduce.

;)

Cooking does denature proteins, making them easier to digest. I don't like eating runny yolks because it feels like they sit in my stomach forever.

I've been eating hard-boiled, slightly undercooked eggs for years. Boiled about 9 minutes, to the point where the outer half of the yolk is solid, but it's still a runny/creamy yolk when you bit into it.