If output buffering is turned off in the C program, there should be no need to pad the output.

Regardless of the presence/absence of "flush()" in the C program, if it is not putting a "\n" at the end of each output iteration, and you don't tailor your perl script to handle its input in some specialized, non-default manner (e.g. by changing the value of the input record separator "$/"), the addition of padding at each output iteration won't help at all.

So don't pad the output, because it's pointless to do that.