I just found this online:
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The presence of whole, undigested seeds in a parrot’s stool is cause for concern. It is usually associated with hyper-motility of the gastrointestinal (digestive) tract — in other words, food is passing too quickly through the system, and digestion is not taking place. The problem usually centers in the glandular stomach (proventriculus) or the gizzard (ventriculus).
A gram-negative bacterial infection, which may be caused by organisms such as Enterobacter mega-bacteria or various spirochetes, is often involved. Fungal infections, and parasites such as Giardia or roundworms, are also possibilities that must be considered. Less frequently, gastrointestinal hyper- motility can arise due to cancer, or to problems in the functioning of the crop and pancreas. The possibility that your bird has contracted the very serious Proventricular Dilation Disease (PDD, or “Macaw Wasting Disease”) must also be investigated (please see reference below).
You should contact your veterinarian if undigested seeds show up in the feces of any species of parrot that you might keep. The first step is usually to submit a fecal sample. This may be followed by a radiograph or, if necessary, a biopsy of the area in question.
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Giardia is something that I keep finding....How is your water supply there?
I lived in India for a chunk of time, and the tap water where I was made lots of people sick (that may not be the case where you are though) . I am not sure if you feed your bird tap water, but if you do and it isn't the safest, that is something to consider...
This is a stretch, but if you have any friends in the health-care world or those who are scientists (or even studying to biologists etc), maybe they could look at the poop under a microscope and tell you is they see any gram negative bacteria or yeast...even a human doctor could TECHNICALLY identify a lot of those things under a microscope in a lot of cases...Obviously they aren't going to do that unless you know them personally (and it would have to be off -the-record) lol, but just thought I'd mention it.
Do you ever share food with your bird after eating from a plate or dish? Do you let your bird touch your lips etc? Your spit can be very harmful to birds, as people carry gram-negative bacteria that birds cannot handle.