We just came across the exact same problem. We sent files to our printer, which we preflighted and showed no issue with any of the images (preflighted in flightcheck as well as indesign) and the file got printed with lo res images. Links showed properly, there were no lo res images included, the paths were leading to the high res yet they printed lo res. When I investigated the file I went to link info and it indicated the the image was 82 k when it was actually 5 megs. Why/how would this occur. Also the only way to get the link to display high res was to relink to file, although they were already linked to correct folder. When the printer ripped the file, the images again were not flagged as missing or lo res and yet that is how it printed. This was a costly error as the piece was a brochure. Fix this problem, or at least explain it PLEASE!! Using CS3 v504, Mac OS 10.5.8. This is very scarey indeed.
Just wandering through, and quite late, but in many ways this sounds like a problem with OPI comments. My recollection is that Quark inserts OPI comments by default and though I've never seen this particular problem, I have seen issues with PDF generated frm Quark files where OPI was active that whne palced into a new ID doc looked fine on screen but printed with missing images.