X6 adds colors to document palette for no apparent reason - can't delete them

Hello,

For some unknown reason X6 adds colors (usually pantone) to the document palette when those colors are not being used - and were never used.

When I try to delete them from the palette I get a message that they are "currently in use" even when nothing other than black is being used.

These offending colors also show up in the pdfs I create from the document.

I have re-recreated the same document page by page, watching the document palette as I go and for no apparent reason colors start to magically appear.

Dos anyone have an idea what is going on here and how to address the issue - other than using InDesign?

FYI, I'm using 64bit X6. Windows 7, 16Gb ram.

Thanks,

K