If your type that appears over a transparency effect seems to be getting fat at output, try moving the type to a new layer above the transparency effect.
If your printer or output device does not support layered PDF files, consider outputting to the PDF/X-1a profile, a flattened format.
Are you seeing off-color frames, white boxes or white outlines around your masked bitmap photos? There are many causes for this. You may not be printing to the right version postscript device. You may be using art with conflicting color profiles or color modes. You may be inappropriately trying to mix spot colors with process colors. You may have ignored the settings in the transparency flattener control dialog.