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
