There are a vairety of reasons I have experienced when this happened. You could have been running an aggressive chemical through the coil that was actually attacking the coil. Usually, when this is happening it means that your galvanization is gone. Acids, DI or Demineralized water, and Bleach will do that.
If that happens, make very sure that you rinse very well, and that you are not getting any residue of the rust in the water. Otherwise, you may end up with little brown rust spots on all the cars, and have some polishing to do.