My first thought was buffer flushing (fflush(stdout)) but I cannot see how a redirection to a file would affect that. In theory there should be no difference between writing to a screen and a file, unless the code calls something like istty(), or checks for screen attributes.
Another possibility is that the shell you are running from is crashing, and never flushes the file buffer, but that is unlikely
I recall some issues using printf from XS when I had to use the PerlIO layers, for example:
PerlIO * debug = PerlIO_open ("debug.txt", "a");
PerlIO_printf(debug, "\nEntry, File: %s\n", szName);
But I have no idea if you need this with your inline code. Can I suggest that you show a small sample of code?
A run of strace or truss (with -f option), or ltrace if you have it, might clarify what is going on.
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