Joe --
The question might be about a common cause, rather than cause and effect. If the immune system is revved up and confused enough to make allergy shots worth enduring, then perhaps it might be revved up and confused enough to be causing other problems, as well.
A quick search indicates there has not been research done to see what kind of link the two (allergies/shots and colitis) might have.
I think this page is a good example of the current state of the science:
http://www.crohnsforum.com/showthread.php?t=37397
Summary: nobody knows. Apparently, nobody's looking.
Through his practice, your rheumatologist may have seen that if the patient has "A", he often has "B", too. But has no research to prove a link much less what type of link. Hence the vague statement.
le
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