What is most likely happening is that part of that transition is trying to write a variable value that has an attribute linked to a custom property in that file. When that happens EPDM tries to write the value to the custom property, but it can only do so with SW 2012 files so it fails. You will continue to see odd issue until you upgrade EPDM to 2013.
I asked my VAR about doing this. We had some users of EPDM on XP but all of our engineers were on Win7. I thought I could keep EPDM at 12 and just upgrade SW to 13. I was told that this will not work. The upgrade path is always EPDM first, then SW. It sounds like you've discovered what happens when the upgrade is done out of order. I do not know for sure what's happening, but I assume that EPDM is digging into your SW13 file and finding things it doesn't know what to do with. I would think that the new file interoperability features of SW13 would make what you are doing possible, but apparently not (or just maybe not for EPDM 13).