How are you seeing the change, on screen or upon export?
Check your Transparency Blend Space, Edit > Transparency Blend Space.
With the separations preview and exported as a press quality pdf.
You may have a profile conflict. Are the color settings the same in both ID and Illustrator? Is the profile embedded in the .ai file? What are the settings policies for missing or mismatched profiles in ID?
Under many circumstances I would expect, and even rely on, ID to keep the color numbers from Illustrator art, but render them acording to the working space of the document, which might well be differnt from the space in which they were created, and under those circumstances I would expect to see some color shifting.
It sounds like you are including a profile with the .ai file that conflicts with your ID doc's profile. Try resaving the .ai without a profile.