Ran into this problem today with InDesign CS5:
I am trying to create a document with only one (spot) color, pantone 293 in this case.
Placed some illustrator files in this document, all of them also only contain pantone 293. However, they also contain some "white" objects. Now my problem appears to be that "white" in illustrator is defined as "0% gray" by default. So when I export my document as PDF from inDesign, i get a PDF with both spot color pantone 293 and black. Strange thing is, I tried making the "white" objects 0% pantone 293 instead of 0% gray, but the PDF still exports with black process color.
Just plain telling my printing company to ignore the black process color altogether would be foolish i guess, since there are objects underneath the illustrator files which need to be knocked out by the "white".
Save the Illustrator file without an embedded profile and place that.
If the problem isn't a profile conflict as Peter suggests, you might try setting up a preflight profile for 1 spot color that will catch uses of CMYK black. When you export a PDF from ID the CMYK channels always exist in the exported PDF, so you may need a preflight check to make sure CMYK plates are empty.
This allows only 1 spot color, defined as Lab. Any use of black would throw an error:
Here the white box is defined as Paper 0|0|0|0 CMYK and I get an error
Defining the box as 0% Orange is OK