Another solution in the brute force category, is there any input that you can give to the C program that will get it to produce output, thereby pushing data out of the buffer?

You may just have to bite the bullet and change the program.

At a guess, you're trying to solve some production issue problem with perl script, but the the C program in question belongs to some other group, is legacy code, or is under "Ivory Tower Source Control", or some other situation that makes modifying it, even with just 1 line of code, difficult.

I know that in certain organizations modifying a legacy program is tougher than passing a bill through Congress, but if they have any kind of tracking system, such as ClearQuest, file the 'Request for an Enhancement', or even elevate it to the level of a bug on the basis of "failure to flush output, prevents programs use with automated scripting tools."