Birds should NOT have yellow urine, as they do not have biliverdin reductase, which is the enzyme that converts biliverdin to bilirubin, and it is the breakdown products of bilirubin (ie, urobilin and stercobilin) that are brown colored (which look yellow when only in dilute concentrations in our urine). These processes are regulated by the liver, via an enterohepatic circulation loop, which we now believe to be important in providing cellular anti-oxidative protective functions. Only a tiny percentage of these pigments are normally excreted into the urine. However, if there are problems with the liver, then large amounts get out from the kidneys, making the urine and urates green or yellow in color. These pigments also deposit in the tissues, including the skin, so macaws, with the bare facial patch, who are suffering from liver failure, have been known to get yellow faces.
However, I wouldn't worry about your bird if its urine is, as you state, at times normal, and only yellow at other times, because you would not get a fluctuating liver condition that alternates between going into and out of liver failure every couple of hours.
Most likely, the cause of the yellow urine is the yellow pigment in her pellets.
But, if your bird has other symptoms or signs of illness, you should take your bird to the avian vet straight away, as some causes of liver failure can kill a bird within a couple of days.
