Which dairy/soy "free" ones did you buy?
The problem is that legally, you can say a food is dairy free if it only has a tiny amount of dairy protein in it - and very sensitive kids react to that. So if the probiotic was grown on a dairy medium, a tiny amount of that dairy sticks to the probiotic, and can cause plenty of problems. Another example - most vitamin C is made from corn, but you see lots of multivitamins with corn-derived vitamin C that say "corn free" - because they contain only very minimal levels of corn protein, so they can legally say that.
Given that your allergist only believes proteins are a problem, I'm guessing she doesn't worry about sourcing a probiotic that isn't grown on dairy.
Also, did the second probiotic contain FOS/inulin? That can also cause very bad reactions for lots of kids, so more than one possible culprit.
And my son never had wonky stools from dairy, gluten, corn, apples, potatoes (he did from salicylates, but that's a different issue). Some kids only have eczema, some only have behavioral reactions, some only have sleep disturbances. Sometimes, the reaction your child has changes - my son used to get stuffy from gluten, then his reaction got purely behavioral.
ETA: Just looked up the ingredients for alimentum. It is 8% soy oil (the powder, 1.1% in the ready to feed version). Again, not soy protein, but lots of kids with food intolerance to soy (vs. food allergy), react to any part of soy, not just the protein. So possibly she's building up a reaction to that. Safflower oil, another ingredient, can cause problems for some - and it has a lot of omega 6 fatty acids, which are inflammatory (so again, you'd perhaps see a build up reaction over time).
I also looked up "casein hydrolysates" - it's milk proteins broken down into smaller proteins, NOT to amino acids. So it's possible she's also sensitizing to these smaller, dairy derived proteins. http://www.cps.ca/english/statements/AL/al94-02.htm