NON EXPERT VIEW
I have noticed ammonia too but not associated with
ALA (I don't use it).
My amateur research says that high
protein diets can pre-dispose to converting excess aminos to ammonia. Livestock (especially pigs - easily noticed coz they live in enclosed spaces) have this problem especially with feeds that are quickly absorbed. Fish also can poison their water because of this.
Farmers seem to reduce likelihood in several ways, here are the two that I could understand:
Use slower absorbed feeds, such as peanut meal,
Stop bullies and gorgers from over feeding (applied to humans that means smaller meals at 2-3 hour intervals). Some texts say that over a certain limit, excess
protein is wasted and broken down into various undesirable products such as ammonia. This limit will vary according to person and their current health etc.. It may be around 60-100grams, so for example 1lb steak /chicken breast at one sitting is probably max if your are feeding 5-6 times per day.
Another possible aid which seems to help on worst days for me is Vit B complex and
glutamine (3 x 5gms e/d)
I'll be following this thread with interest...thanks for bringing it up!