How sudden is this pH crash?
You mentioned it happening twice over a 4 month period. Is the pH going from 7.8 to 6 (or less) overnight? Over a two day period? Weeks time? In a month? 7.8 gradually lowering to 6 in two months?
As Diana mentioned, organic matter and decomposition by microorganisms lead to the water turning more acidic.
But as far as I know, microorganisms produce co2. Not sure which microogranisms take carbon from carbonates.
If 7 juvi boesemani in the 55 gallon is all you have, that's not much of a fish bioload by itself to contribute to the pH lowering as quickly as it is.
How is your maintenance on the tank? Tank very dirty? Filter very dirty? How often do you clean out the filter? How often do you vacuum the substrate (mulm, detritus, etc)? How often do you do water changes and what %?
I take it you are not injecting co2, correct?
What kind of plants do you have? Any fast growers?
How many hours do you leave the light on?
Plants can resort to stripping carbon from the KH (thus lowering KH) if they have no other option.
I've heard others mention that higher CEC substrates, Eco Complete being one of those, can strip away carbonates from the water (lowering KH). I don't know too much about that. I am wondering if the KH/PH is higher near the substrate (not much, slowly leaching out into nearby lower water), explaining why the fish are hanging at the bottom since they find that area more comfortable for them. Fish in water pH not to their liking don't just stay at the bottom of the tank, they still will venture around the tank, though a lot less active, often just hovering around. Haha just a wild "what if" though. I wonder just how much KH they would strip until they are "saturated", though it should stabilize very soon by now.
Is there any driftwood in the tank that is leaching out a lot of tannins or is rotting?
By the way, if you are referring to dwarf shrimp such as Neocaridina Red Cherry Shrimp, they will probably be eaten by the rainbows, especially when the boesemani are adults, even the adult shrimp will likely be gone.