The issue is that while you may have element(s) with transparency, they could be element(s) created within InDesign (say, a vignette box for overlaying type on an image), composited Photoshop image(s) or Illustrator vector art with transparent and/or blended effects. It could be any one of those issues, or any multiple of them.
Without seeing the file, and seeking out the elements one-by-one (for your placed graphics, selecting them individually and using the Edit>Edit Original command will help immensely), then correcting them, there's really no way for us to help. The fastest way out for you, I suspect, would be to find an experienced designer and try to hunt down the offending items one by one, then re-uploading the job until everything is fixed and the job takes.
Wish I had better news for you. This isn't going to be an easy one for you, I'm afraid.
Randy