I assume then you do not have the license for proofing in MetaDimension (ColorProof Pro, ColorProof __).
Therefore the problem is most likely caused by the process you are ripping the data of the PDF. In this method of output typically your Mac or PC has a postscript driver that converts the document or in this case PDF data to the postscript language then communicates this data (via firewire, ethernet, usb) to the printer which inputs this postscript communique and outputs raster data on the fly. Typically the postscript driver on your Mac or PC causes a problem like this to occur in the PDF to postscript conversion or the printer itself doesn't understand the postscript data it is trying to interpret and causes an error like this to occur.
So what is the solution?
Open the PDF in photoshop and rasterize it to ___ PPI (anything beyond 600 is total overkill for traditionally marketed litho). If the problem occurs in Photoshop rasterizing then you've got a problem PDF and I would recommend trying PDF/X format upon exporting from InDesign. If that doesn't fix it you have a seriously nightmarish file.
What is scary about this method of proofing?
Your proof is really a softproof and not a real proof. The RIP at MetaDimension can interpret completely different results than your proofer (for better or worse). I am not a gambling man in any sense of the word but I would put money on the plates for this job coming out of the other MetaDimension without this problem. If you want accurate proofs the plates and the proofer HAVE to come out of the same RIP. Your proofs are also most likely not even close to color accurate.
What is the long term solution?
Like yourself I have found my self in this same situation before. For reasons of cost Heidelberg sales will sell you (or most likely your boss) Printready P (the most budget version of printready/prinect workflow) without an actual proofing module built into MetaDimension. The module costs I believe is $5,000 - $10,000 and it is basically an combination of an EFI program called ColorProof (RIP to Proofer interpreter) and a device output license within MetaDimension. My former boss couldn't see the value in this investment after dropping well over $100k on a new workflow, epson9800 and suprasetter that had essentially no actually accurate proofing solution. Buy it if you are the boss or tell your boss to buy it. If your company does not buy the proofing licensing you will continue to have these problems and will continually have to rasterize files manually in Photoshop so that your softproof will come out looking "correct". The risk will always be that it proofs correctly but will RIP incorrectly and bad plates will ensue.