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
I agree with what Rob says. I had this issue today. To fix the overprint issue, your setting for Compatibility should be Acrobat 4 PDF 1.3
Then click on the Advanced option on the left side menu. You should see the Overprint and Transparency Flattener Options for pdf 1.3 only. Under Preset drop down (High Resolution) should be selected. This will enable your gradient and mesh resolution to print at 300 ppi. If you have further concerns, you can hit the Custom button and change the ppi to whatever setting you need it to be,
I hope this helps. I have Adobe CS5.