Ear infections can be related to immune system weakening. If you are vaccinating, you may want to check out www.generationresuce.com or www.theeducatedparent.blogspot.com. Flu vac is ineffective and dangerous, don't do it, you could make an existing problem much worse. For now:
Try giving proibotics at night (Whole foods sells), culturelle once a day (whole foods, wal-greens) and cod liver oil (one tsp a day). Limit wheat and consider giving Almond milk with cod liver oil for fat rather than formula or milk. Cod liver oil has vit A and vit D which fight virals and imflamation, and will go a very far way to prevent the flu. If he improves over a 2 week - 1 month period, you will know the digestive issues are there. If not, you have just made him much healthier. Both my kids started the ear infections at 7 months and 13 months (not a coincidence it was 1 month after a round of vac's). The first, I ignored, and learned a very hard lesson. The second, I got smart and learned how to treat. Both are now healthy and vibrant after a return from some tough times.
Best of luck, J.