I just now printed the above post to see what the screenshot would do with the X. (Sorry, couldn't edit the post.) Save your trees: the X is consistent in grayscale! Maybe that's a clue? Should I dump this illustration in Fireworks or something and then import it to ID?
Make sure the document color space and everything you place as art in the document have the same colorspace. Look at InDesign's Edit menu > Transparency Blend Space and make sure you choose either RGB or CMYK and that placed graphics are the same sort of color model.
I changed the Illustrator drawing, with X over it, to CMYK, as that is what's used in the ID doc. The X shade over the gradiant is darker than it was before, but still not the same shade as the rest of the X. I can probably live with this(don't know about my readers!), but wonder if there is anything else I can try?
I just now thought to print the drawing from Illustrator, and the grayscale contrast in the X is showing up there. I will go to the Illustrator forum and see if someone there has any more ideas. I'll post links here to anything more that I find over there. Thank you.