I'm using InDesign CS6 and when i do an export my document to pdf some of the images in it turn blue.
This looks like a profile conversion. Your image is a screen capture, so most likely still RGB, but the PDF/X-1a prest converts to CMYK. Can you show us the output section of the export settings, please.
I have seen this in the distant past (and before I ever used ID). I cannot remember what it was now, though.
Can you put one of the actual images into a ZIP file and upload it somewhere and post a link?