The mentione box might either this: http://indesignsecrets.com/eliminating-ydb-yucky-discolored-box-syndrome.php
Or you choosed in the import options (place dialog) not to have transparency or your frame is white.
Images with transparency are best imported as PSD, never use EPS in InDesign PNG is not good for print.
I am then exporting as a pdf and printing. In both Indesign and the pdf on screen the image looks perfect, transparent background, however once it prints the image has a white box around it.
If both the PDF and InDesign previews look fine then your printer is not handling the flattening of the page correctly when you print the PDF with live transparency. Try flattening the PDF when you export—set the Compatibility to Acrobat 4, or if it's ok to convert all color to CMYK export using PDF/X-1a