I've spent over a year now consuming, experimenting with and studying kefir and its effects on my health. Keep in mind these are just my thoughts as they have related to me, so your mileage may vary...

1. Kefir is alive. If you consume kefir around a meal with carbs, simple or complex, the bacteria and molds in the kefir will dine to a massive extent. That is where the bloating comes from. If you eat with a protein meal, they still eat (that is their purpose, to digest your food for you) but much more slowly. Kefir is CO2 forming, the gas is CO2, and yes, it comes out both ends with a carb meal! After consuming kefir for many months I learned that I had to be careful of carbs because kefir actually attaches to the lining of your digestive track. That’s it’s “history”, kefir is in effect an amplification of the bacteria and molds in mothers milk which in turn is intented to establish the digestive track and much of the immune system. And so after consuming kefir for a long time they line your digestive track, and any carb meal with then trigger the problem. Put another way kefir tends to force you towards a protein diet and reduce your carbs. And many suggest that is a good thing. ;) 

They are right to an extent.  Yes, the bacteria feed on fibers.  More precisely they ferment the fibers to break down the long chain sugar molecules in to simpler sugars they can feed on.  During the fermentation process gasses are produced.  

But kefir is best taken on an empty stomach, not with food.  Spices and other compounds in foods and drinks could kill the bacteria, as well as the acid increase during digestion.

Agree that kefir can produce gas in the presence of excess carbohydrates, however this seems to be more prevalent when carbohydrates are consumed without any fiber.  It is my opinion that regardless of whether kefir is consumed with carbs, if the bowel is moving on a regular basis (from whole food/higher fiber intake) then fermentation that takes place in the gut is minimized. I regularly use homemade, double fermented kefir in whole food smoothies that generally include raspberries, avocado, banana, leafy greens and sprouts and do not experience any digestive discomfort.  I would hesitate to combine kefir with straight fruit juice or high glycemic foods only.

      2.   i’ve been drinking kefir smoothies for breakfast every day since i got my grains a few months ago!
            For bloating/gas: try taking an enzyme to help digest the proteins and fats in the kefir. My doctor has me taking chewable papaya  enzymes with every meal–even if i just have the kefir. it helps a lot. i used to get             sharp pains in my abdomen from gas and i don’t  get those any more since taking the enzyme. (There are other types of digestive enzymes out there too–papaya might not be the  best one for you!) on the other hand, some peoples’ bodies just cannot accept the kefir because some bodies are very sensitive to  fermented things. so if your body doesn’t respond well to wine and beer, it may not respond well to the kefir either. Kefir is very nutritious…but you need to decide if the health benefits outweigh the risks for  YOUR body.

Enzymes can digest the bacteria, so they kind of defeat the purpose.  Although chewable papaya actually has very little enzyme in it.  Green papaya is high in enzymes, but the levels drop drastically with ripening.

The bacteria in kefir are the ultimate enzyme supplement for digestion, so adding extra enzymes to combat what the kefir is doing doesn't make a lot of sense.  When first starting kefir, it seems common among myself and my friends to experience a lot of gas.  I attribute this to the fact that the kefir bacteria are establishing themselves, propagating, and eradicating "bad bacteria." If colonies of other kinds of bacteria are dying off (such as with Candida) this has been shown to produce excessive amounts of gas while the body is eliminating it. Some people seem to do better by starting slowly, with 1/2 cup a day and working up to a couple of cups. Within approximately 1-2 weeks symptoms of bloating/gass dissappeared for me.  It is worth nothing that if I stop drinking kefir for longer than 1 week and then reintroduce it, such symtoms reoccur but are far more mild - something I attribute to the kefir colonies re-establishing themselves.

 3.  Do  NOT use it if you have any condition that might reduce your immune function. (I have Hep C)

Do these make sense to you? Any other good explanations?

#3 makes absolutely no sense at all.  The flora make up about 80% of the immune system, so it only makes sense to maintain the flora in cases of immune suppression.  Otherwise you would only be suppressing the immune system further, which is not good at all.

I have Sjogren's with Lupus overlap, Fibro and Hashimoto's. I have lived with these diseases for 10 years. After drinking Kefir for over a year all symptoms of my diseases are gone, I am off all medication and my bloodwork shows normal levels of inflammation where a year ago my inflammation was so high it could not be measured.  I drink 1-2 cups a day.  Also, in all of that time I have weathered 3 separate flus in my family and I haven't been sick once, not even with a sniffle, despite the fact that a year ago I survived on daily OTC sinus medication and prescription anti-biotics for recurrent respiratory and sinus infections. There is absolutely no doubt in my mind that kefir, coupled with a whole foods, high Raw diet has been crucial in healing my body.

In addition to healing my auto-immune issues, kefir has been instrumental in a few other ways too.  I have healed a plantar wart in less than 3 weeks - it had existed for nearly a year before that and would not respond to other topical treatments.  For ladies, kefir is an excellent home remedy for yeast infections, bringing immediate relief.  I've also used it as a a facial wash. I also dilute it and use it in my garden.

Or is it just  herxheimer´s effect and I should hang on until it clears? If so, for how long?

I still think it is the high calorie content causing the weight gain.  You can try water kefir instead, which has a lot less calories.  As for the bloating taking it well before meals should cut way down on the bloating.

Do you exercise?  Do you have hormonal imbalance issues? What other foods are you eating?  I would say 2 cups of whole milk kefir by itself would not cause weight gain unless there are other factors, such as eating too many high calorie, high glycemic other foods.  I eat a high raw diet (85% raw) with whey protein, 2 cups of whole raw milk kefir daily, and probably 15-20 servings of fruit and vegetables. I try to choose fruits and veggies that are low-glycemic, high fiber and high fat. Eating all of this, I generally average around 1200-1500 calories a day and that is usually packing it in for me, and with little exercise I was able to lost about 40 pounds at the beginning of this diet.  Depending on your activity level and caloric needs, you may consider reducing how much you consume outside of the vegetables and fruits and focusing on low-glycemic and non-starchy vegetables (stay away from potatoes, for example.)

Or, if it is actually fermanetation due to the sugars in my fruit meal, should I take it before eating or even going down on the amount?

Yes.

I tend to prefer drinking it on an empty stomach, but that's just because I like the taste.  I've heard that kefir takes on average 45 minutes to digest, so if you are worried about fermentation from other foods you may consider factoring in digestion time to reduce that component. Again, starting off with a small amount seems to be helpful for easing into a daily dose.

Anybody with a similar experience that got over it by not stopping to drink it?