Quel est le paramètre d'export ? Quel type d'imprimante ?
C'est peut-être lié à ça :
voir aussi cette discussion :
Can you confirm how os the logo 'cut out'?
Can you try an alternative method? it could be transparent png, a saved selection as a channel in photoshop then used in InDesign...
I had similar issues in the past where the cut-out did not print as expected. just a save as something else in Photoshop, then re-imported in InDesign solves it.