Hi,
Also try bp kids so you can talk to other parents:
http://www.bpkids.org/site/PageServer

A doctor who works with multiple issues related to allergies could be a good source of information/help.

The allergy shots are not supposed to interfere with medication. But I can imagine that they could throw off a sensitive immune system. Bipolar can be triggered at onset and then made worse through its course through stressors.

Did he continue the shots?
Have you been able to identify food (and other) allergies/sensitivities?
Have you been able to eliminate allergies?

Some books discuss ameliorating bipolar by use of vitatmins and supplements. Others, by avoiding allergens:
--The Natural Medicine Guide to Bipolar Disorder by Stephanie Marohn
--Nutrition and Mental Illness: An Orthomolecular Approach to Balancing Body Chemistry by Carl C. Pfeiffer
--Brain Allergies: The Psychonutrient and Magnetic Connections by Willam H. Philpott, William H. Philpott MD, et al

There are others, as a quick search of amazon will show you.

These ways of thinking are starting to show up in the science. but I can't site scientific sources for you write now. I think that the books have bibliographies for further reference.
Mari