Answering my own question, it could be that the pH is changing during the ion exchange resin pull? I've been setting up the pH before it goes into solution. This could be an issue for sodium carbonates because if Na+ replaced what is being eluted, since some of the biological molecules should have the form XH+, that could liberate H+ and the liberated H+ would neutralize the elution. Ammonia could be a little more resilient to this the way I was doing things.

For example (R- represents the negatively charged cation resin functional group)

NaHCO3 + R-XH+ -> H2CO3 + X + R-Na+, this generates carbonic acid which neutralizes the elute and stops elution.

So, this is simply a case of me being inexperienced with ion resins. The answer is simple, monitor the pH during the ion resin pull.