I am working on treatment of textile waste water. I have found that the presence of carbon in a large amount caused an increase in NO3-N in outflow under aerobic and anaerobic condition, while, there is a removal in NH4-N.
Unfortunately I cannot explain why an increase in carbon would increase the nitrate in your outflow. Ammonia is oxidised to nitrate in aerobic conditions which is then reduced to nitrogen gas in anoxic (no dissolved oxygen present) conditions. It may be co-incidental that increased nitrate corresponded to high carbon concentrations and the real reason was an increase in flow rate causing a reduction in the anoxic detention period or dissolved oxygen carry-over.
Alternatively, it might be that the high carbon levels were associated with an increase in the concentration of potential toxic chemicals present in dyes (eg potassium azide) resulting in these chemicals exceeding their inhibitory threshold. However, most of these toxic chemicals also inhibit oxidation of ammonia.