Most likely not mold. There are biocide compounds to prevent proliferation in commercial inks. Take a look at the registered patent for that ink manufacturer or msds. Having said that... Time, environment, and air exposure to ink can do some wild things.
First assumption is the ink has coagulated or changed viscosity over time. You say it is a re-filled cartridge and old inks. Most likely it has thickened and coagulated.
Best to flush the system from the cartridges to the print head dampers. Then flush the dampers. With fresh inks, or cleaning solution on your re-fill able cartridges run initial fill so the system can flush the print head.
That is, if you are convinced these contaminates are in your ink lines.