Support for the 5dmk3 came with LR4.1. This version is now obsolete, so you will need to upgrade to LR5. You could also download the free DNG Converter and convert your cr2 to dng, which could be used with LR3.
Why did it stop working all of the sudden. I have had the 5dmk3 for almost a year and I have not had this problem with my current lightroom. Are the DNG files lossy files? Can you work with them with out losing info?
I don't see how it could have stopped all of a sudden, as LR3 has never supported the 5dmk3. I know from personal experience, as I have one. The DNG file is lossless, so you will not lose any info!