After 50% water changes, all of the fish are showing signs of stress, such as rapid respiration. I am currently using the EI index for dosing ferts and traces as well and injected CO2. Any idea as to what is causing this? The local fish guy thinks it might be a ph swing? My setup is as follows:

29 gal
3.5 watts per gal lights on ten hour timer
eheim canister filter
Pressurized CO2 on one half hour before lights and off one half hour before lights out.