Thanks for adapting the smaller example. I think I figured out what's 
the problem.

The error reported by checkfile.c is 0x20 = ERROR_SHARING_VIOLATION
"The process cannot access the file because it is being used by 
another process."

I modified the subprocess call, adding the parameter close_fds=True -- 
and now I see no errors. 
Please do a similar change in your application and see if it works.