So far I cannot detect any difference between the two input feature classes other than that anything in pre 10.2 copy features will work. If I set the input to be a FC from a 10.2 file GDB, I get the 'ol 000210 error. Projections aren't an issue, both inputs reside in the same level of the file structure, no differences in OS permissions. I've created a fresh fGDB for testing, same behavior. I can even have both FC versions in the same MXD and just switching the input in the model decides success or failure.
To be fair, when i say non-10.2 GDB, my older ones are almost all 9.3. I'll try to test with an intermediate version as well. I have tested with different output locations and no problems there. Its odd because the error raised is related to output...not input. I am currently writing to %scratchFolder%.
Has anyone seen similar if not identical behavior from this? Again, it appears to only affect 10.2 fGDB using the copy features tool.