I figured it out! After looking at each individual variable (nitrates, pH, possibly contaminated wood from the local river, phosphates, excel, flourish, prime, tap water, rain water, substrate, etc), I figured out that it was KCl. I used to dose KCl to excess, at about 2-3 tablespoons for my 55 gallon. Since I stopped doing this (with many WC), I've been able to keep ghost shrimp and MTS for months. Perfectly healthy.
Now, I don't think it was an overdose of K+ that did it. I've also since seen anecdotal evidence that Cl- ions in excess are potentially bad for freshwater invertebrates.
Hopefully other hobbyists can use this information for maintaining the health of their own tanks.
Just to be sure; my tank is low-light and low-tech. It's possible that high-tech tanks have plant growth rates that utilize Cl- ions quickly enough to make the water MTS safe. Interestingly, my ramshorns never had much of a problem surviving. Now they are reproducing much more quickly. Also, the pygmy corys are spawning like mad!