I'm guessing it's something about buffering , but I'm not sure.

It isn't. Note that you're doing chomp($ans=<STDIN>); in your perl code, while you're not doing anything like that in the C code.

#include <stdio.h>

int main() {
        char answer=' ';

        printf("(F)irst,(S)econd,(T)hird\n");

        scanf("%c",&answer);

        while(answer !='F' && answer !='S'  && answer !='T') {
        printf("answer was: '%c', which is not what I want\n",answer);
                printf("(F)irst,(S)econd,(T)hird\n");

                scanf("%c",&answer);
        }

        return 0;
}
[download]

Gives:

$ ./a.out 
(F)irst,(S)econd,(T)hird
a  
answer was: 'a', which is not what I want
(F)irst,(S)econd,(T)hird
answer was: '
', which is not what I want
(F)irst,(S)econd,(T)hird
[download]