I have been working with my re-seller to fix the issue since October of 2012 with the above error. I realize that you are aware of this issue and I have went through several posts to come up with a fix myself. I am just curious why checking in files worked fine before Autodesk 2013 was installed. Every now and then the process will work, but it is usually a waste of my time to try.
I did just find that I can check in a blank file to vault (who knows, that may not always work, I will let you know). Doing this allows me to begin checking in other files, but come on, why is there no fix yet! I should not be spending 6 months to try to find out how to fix the issue, not to mention all the time it will take me to check in the files that need to be added to Vault once the issue has been resolved (if that ever happens).
Am sorry to hear that you have an ongoing serious issue here, without understanding the exact details of your case all I can really do is explain the process we follow here to resolve this type of issue, firstly though can you confirm that you have an Autodesk support case logged for this error and perhaps share what the status is - has support been able to replicate your issue or provide any suggestions?